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- PDB-6zmw: Structure of a human 48S translational initiation complex -

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Database: PDB / ID: 6zmw
TitleStructure of a human 48S translational initiation complex
Components
  • (40S ribosomal protein ...) x 31
  • (Eukaryotic translation initiation factor ...) x 19
  • 18S rRNA18S ribosomal RNA
  • 60S ribosomal protein L41
  • Eukaryotic initiation factor 4A-I
  • Initiator Met-tRNA-i
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • mRNAMessenger RNA
KeywordsTRANSLATION / ribosome / initiation complex
Function / homology
Function and homology information


regulation of polysome binding / positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / cap-dependent translational initiation / cellular macromolecule biosynthetic process / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress ...regulation of polysome binding / positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / male germ cell proliferation / translation initiation ternary complex / glial limiting end-foot / cap-dependent translational initiation / cellular macromolecule biosynthetic process / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / negative regulation of translational initiation in response to stress / positive regulation of translation in response to endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of mRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / mRNA cap binding / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / positive regulation of miRNA mediated inhibition of translation / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 2B complex / deubiquitinase activity / translation factor activity, RNA binding / multi-eIF complex / eukaryotic translation initiation factor 3 complex / cytoplasmic translational initiation / RNA cap binding / eukaryotic 43S preinitiation complex / eukaryotic translation initiation factor 4F complex / PERK-mediated unfolded protein response / positive regulation of respiratory burst involved in inflammatory response / negative regulation of guanyl-nucleotide exchange factor activity / nucleolus organization / protein tyrosine kinase inhibitor activity / mammalian oogenesis stage / protein-synthesizing GTPase / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / developmental process / negative regulation of RNA splicing / cellular response to nutrient levels / IRE1-RACK1-PP2A complex / eukaryotic 48S preinitiation complex / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / ubiquitin ligase inhibitor activity / laminin receptor activity / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of cell division / activation-induced cell death of T cells / negative regulation of endoplasmic reticulum unfolded protein response / regulation of cellular response to stress / negative regulation of hydrogen peroxide-induced neuron death / positive regulation of base-excision repair / negative regulation of DNA repair / response to TNF agonist / oxidized pyrimidine DNA binding / positive regulation of DNA N-glycosylase activity / negative regulation of ubiquitin protein ligase activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / regulation of translational initiation / NF-kappaB complex / negative regulation of phagocytosis / regulation of establishment of cell polarity / positive regulation of endodeoxyribonuclease activity / signaling adaptor activity / negative regulation of Wnt signaling pathway / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / protein kinase A binding / positive regulation of mitochondrial depolarization / supercoiled DNA binding / translation regulator activity / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / phagocytic cup / ion channel inhibitor activity / negative regulation of smoothened signaling pathway / positive regulation of apoptotic signaling pathway / erythrocyte development / ubiquitin-like protein conjugating enzyme binding / iron-sulfur cluster binding / TOR signaling / positive regulation of cellular component movement / fibroblast growth factor binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / rescue of stalled ribosome / negative regulation of peptidyl-threonine phosphorylation / positive regulation of T cell receptor signaling pathway / poly(U) RNA binding / regulation of presynapse assembly / stress granule assembly / monocyte chemotaxis / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity
Translation initiation factor eIF3 subunit / Ribosomal protein S4e, N-terminal / MIF4G-like domain superfamily / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Initiation factor eIF2 gamma, C-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic ...Translation initiation factor eIF3 subunit / Ribosomal protein S4e, N-terminal / MIF4G-like domain superfamily / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / K homology domain-like, alpha/beta / WD40/YVTN repeat-like-containing domain superfamily / Initiation factor eIF2 gamma, C-terminal / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S6, eukaryotic / RNA helicase, DEAD-box type, Q motif / Helicase superfamily 1/2, ATP-binding domain / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor 3 subunit J / Ribosomal protein S4e, central region / Ribosomal protein S5, N-terminal / Translation initiation factor IF2/IF5, N-terminal / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Ribosomal protein S13/S15, N-terminal / Nucleic acid-binding, OB-fold / Tetratricopeptide-like helical domain superfamily / DEAD/DEAH box helicase domain / Translation initiation factor 2, alpha subunit / Eukaryotic translation initiation factor 3 subunit B / Zinc-binding ribosomal protein / Ribosomal protein S13-like, H2TH / Eukaryotic translation initiation factor 3 subunit K / S15/NS1, RNA-binding / K homology domain superfamily, prokaryotic type / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Armadillo-type fold / Translation initiation factor IF2/IF5, zinc-binding / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Ribosomal protein S3, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S9, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S17, conserved site / Ubiquitin domain / Ubiquitin conserved site / WD40 repeat, conserved site / Translation initiation factor 3 complex subunit L / Eukaryotic translation initiation factor 3 subunit E, N-terminal / Ribosomal protein S8e, conserved site / Ribosomal protein S6e, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S21e, conserved site / Eukaryotic translation initiation factor 3 subunit E / Ribosomal protein S19e, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S2, conserved site / Translation initiation factor 1A (eIF-1A), conserved site / Ribosomal S11, conserved site / Ribosomal S24e conserved site / Ribosomal protein S4, conserved site / WD40-repeat-containing domain / Eukaryotic translation initiation factor 3 subunit G / Translation protein, beta-barrel domain superfamily / Ribosomal protein L41 / Ribosomal protein S4/S9 / Ribosomal protein S5 / Ribosomal protein S10 / WD40 repeat / Helicase, C-terminal / Ribosomal protein S3Ae / Ribosomal protein S6e / Ribosomal protein S3, C-terminal / Ribosomal protein S19e / Translation initiation factor 1A (eIF-1A) / Ribosomal protein S17e / Ribosomal protein S14 / Ribosomal protein S8e / Ribosomal protein S26e / Ribosomal protein S4e / Translational (tr)-type GTP-binding domain / Ribosomal protein S13 / Ribosomal protein S9 / Proteasome component (PCI) domain / Ribosomal protein S8 / ATP-dependent RNA helicase DEAD-box, conserved site / Ubiquitin-like domain / Ribosomal protein S27 / Ribosomal protein S15 / JAB1/MPN/MOV34 metalloenzyme domain / Ribosomal protein S7e / Ribosomal protein S12e / RNA recognition motif domain / Ribosomal protein S28e / Ribosomal protein S17/S11 / Ribosomal protein S5/S7 / Ribosomal protein S2 / Ribosomal protein S4/S9, N-terminal / Eukaryotic translation initiation factor 3 subunit D
40S ribosomal protein S15 / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit D / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S24 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / Eukaryotic translation initiation factor 3 subunit H ...40S ribosomal protein S15 / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit D / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S24 / 40S ribosomal protein S29 / 40S ribosomal protein S18 / Eukaryotic translation initiation factor 3 subunit H / 40S ribosomal protein S6 / 40S ribosomal protein S5 / 40S ribosomal protein S23 / 40S ribosomal protein S14 / 40S ribosomal protein S16 / 40S ribosomal protein S25 / Eukaryotic translation initiation factor 3 subunit F / 40S ribosomal protein S8 / 40S ribosomal protein S7 / 40S ribosomal protein S3a / 40S ribosomal protein S20 / Eukaryotic initiation factor 4A-I / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit B / 40S ribosomal protein S15a / Eukaryotic translation initiation factor 3 subunit J / 40S ribosomal protein S26 / 40S ribosomal protein S12 / gb:174924: / Eukaryotic translation initiation factor 3 subunit L / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 1A, X-chromosomal / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit A / 40S ribosomal protein S27 / Eukaryotic translation initiation factor 1 / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 2 subunit 3 / 40S ribosomal protein S19 / 40S ribosomal protein S3 / 40S ribosomal protein S28 / Eukaryotic translation initiation factor 4 gamma 1 / Receptor of activated protein C kinase 1 / Eukaryotic translation initiation factor 2 subunit 2 / 40S ribosomal protein S2 / 40S ribosomal protein S21 / 40S ribosomal protein SA / Ubiquitin-40S ribosomal protein S27a / 60S ribosomal protein L41 / 40S ribosomal protein S30 / 40S ribosomal protein S17 / Eukaryotic translation initiation factor 2 subunit 1 / 40S ribosomal protein S9 / 40S ribosomal protein S10
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBrito Querido, J. / Sokabe, M. / Kraatz, S. / Gordiyenko, Y. / Skehel, M. / Fraser, C. / Ramakrishnan, V.
Funding support United Kingdom, United States, 3items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release

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Assembly

Deposited unit
2: Eukaryotic translation initiation factor 3 subunit I
1: Eukaryotic translation initiation factor 3 subunit B
6: Eukaryotic translation initiation factor 3 subunit M
4: Eukaryotic translation initiation factor 3 subunit F
u: Eukaryotic translation initiation factor 3 subunit A
v: Eukaryotic translation initiation factor 3 subunit E
S: 40S ribosomal protein S6
y: Eukaryotic translation initiation factor 3 subunit C
8: Eukaryotic translation initiation factor 3 subunit H
G: 40S ribosomal protein S7
H: 40S ribosomal protein S27
K: 40S ribosomal protein S21
L: 40S ribosomal protein S2
O: 40S ribosomal protein S3a
N: 40S ribosomal protein SA
Q: 40S ribosomal protein S26
P: 40S ribosomal protein S14
I: 40S ribosomal protein S13
x: Eukaryotic translation initiation factor 3 subunit D
3: Eukaryotic translation initiation factor 3 subunit K
5: Eukaryotic translation initiation factor 3 subunit L
7: mRNA
9: 60S ribosomal protein L41
A: 18S rRNA
B: 40S ribosomal protein S11
C: 40S ribosomal protein S4, X isoform
D: 40S ribosomal protein S9
E: 40S ribosomal protein S23
F: 40S ribosomal protein S30
r: Eukaryotic translation initiation factor 2 subunit 1
J: 40S ribosomal protein S15a
R: 40S ribosomal protein S8
T: 40S ribosomal protein S24
V: 40S ribosomal protein S5
Y: 40S ribosomal protein S16
Z: 40S ribosomal protein S3
a: 40S ribosomal protein S10
b: 40S ribosomal protein S15
c: Receptor of activated protein C kinase 1
d: 40S ribosomal protein S19
e: 40S ribosomal protein S25
f: 40S ribosomal protein S18
i: 40S ribosomal protein S29
k: Ubiquitin-40S ribosomal protein S27a
m: 40S ribosomal protein S12
n: 40S ribosomal protein S28
o: Eukaryotic translation initiation factor 3 subunit G
p: Eukaryotic translation initiation factor 1
q: Eukaryotic translation initiation factor 1A, X-chromosomal
z: Eukaryotic translation initiation factor 3 subunit J
M: 40S ribosomal protein S17
h: 40S ribosomal protein S20
s: Eukaryotic translation initiation factor 2 subunit 2
w: Initiator Met-tRNA-i
t: Eukaryotic translation initiation factor 2 subunit 3
j: Eukaryotic initiation factor 4A-I
g: Eukaryotic translation initiation factor 4 gamma 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,403,160148
Polymers2,400,86657
Non-polymers2,29491
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Eukaryotic translation initiation factor ... , 19 types, 19 molecules 2164uvy8x35ropqzstg

#1: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting ...eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / TGF-beta receptor-interacting protein 1 / TRIP-1 / eIF-3-beta / eIF3 p36


Mass: 36543.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13347
#2: Protein Eukaryotic translation initiation factor 3 subunit B / eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / ...eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / eIF3 p110 / eIF3 p116


Mass: 92593.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55884
#3: Protein Eukaryotic translation initiation factor 3 subunit M / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7L2H7
#4: Protein Eukaryotic translation initiation factor 3 subunit F / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF- ...eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 37593.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00303, ubiquitinyl hydrolase 1
#5: Protein Eukaryotic translation initiation factor 3 subunit A / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


Mass: 166903.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14152
#6: Protein Eukaryotic translation initiation factor 3 subunit E / eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 ...eIF3e / Eukaryotic translation initiation factor 3 subunit 6 / Viral integration site protein INT-6 homolog / eIF-3 p48


Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60228
#8: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99613
#9: Protein Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


Mass: 39979.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15372
#19: Protein Eukaryotic translation initiation factor 3 subunit D / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15371
#20: Protein Eukaryotic translation initiation factor 3 subunit K / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / ...eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


Mass: 25083.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBQ5
#21: Protein Eukaryotic translation initiation factor 3 subunit L / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 66803.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y262
#30: Protein Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 36161.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05198
#47: Protein Eukaryotic translation initiation factor 3 subunit G / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Eukaryotic translation initiation factor 3 subunit 4 / eIF-3-delta / eIF3 p42 / eIF3 p44


Mass: 35662.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75821
#48: Protein Eukaryotic translation initiation factor 1 / eIF1 / A121 / Protein translation factor SUI1 homolog / Sui1iso1


Mass: 12752.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1, SUI1 / Production host: Escherichia coli (E. coli) / References: UniProt: P41567
#49: Protein Eukaryotic translation initiation factor 1A, X-chromosomal / eIF-1A X isoform / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 16488.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1AX, EIF1A, EIF4C / Production host: Escherichia coli (E. coli) / References: UniProt: P47813
#50: Protein Eukaryotic translation initiation factor 3 subunit J / eIF3j / Eukaryotic translation initiation factor 3 subunit 1 / eIF-3-alpha / eIF3 p35


Mass: 29108.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3J, EIF3S1, PRO0391 / Production host: Escherichia coli (E. coli) / References: UniProt: O75822
#53: Protein Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit beta / eIF-2-beta


Mass: 38454.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P20042
#55: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 51178.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41091, protein-synthesizing GTPase
#57: Protein Eukaryotic translation initiation factor 4 gamma 1 / / eIF-4G1 / p220


Mass: 145733.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4G1, EIF4F, EIF4G, EIF4GI / Production host: Escherichia coli (E. coli) / References: UniProt: Q04637

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40S ribosomal protein ... , 31 types, 31 molecules SGHKLONQPIBCDEFJRTVYZabdefimnMh

#7: Protein 40S ribosomal protein S6 / / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62753
#10: Protein 40S ribosomal protein S7 / / Small ribosomal subunit protein eS7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62081
#11: Protein 40S ribosomal protein S27 / / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P42677
#12: Protein 40S ribosomal protein S21 / / Small ribosomal subunit protein eS21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63220
#13: Protein 40S ribosomal protein S2 / / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P15880
#14: Protein 40S ribosomal protein S3a / / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61247
#15: Protein 40S ribosomal protein SA / / 37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin ...37 kDa laminin receptor precursor / 37LRP / 37/67 kDa laminin receptor / LRP/LR / 67 kDa laminin receptor / 67LR / Colon carcinoma laminin-binding protein / Laminin receptor 1 / LamR / Laminin-binding protein precursor p40 / LBP/p40 / Multidrug resistance-associated protein MGr1-Ag / NEM/1CHD4 / Small ribosomal subunit protein uS2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#16: Protein 40S ribosomal protein S26 / / Small ribosomal subunit protein eS26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62854
#17: Protein 40S ribosomal protein S14 / / Small ribosomal subunit protein uS11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62263
#18: Protein 40S ribosomal protein S13 / / Small ribosomal subunit protein uS15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62277
#25: Protein 40S ribosomal protein S11 / / Small ribosomal subunit protein uS17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62280
#26: Protein 40S ribosomal protein S4, X isoform / Ribosome / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29654.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62701
#27: Protein 40S ribosomal protein S9 / / Small ribosomal subunit protein uS4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46781
#28: Protein 40S ribosomal protein S23 / / Small ribosomal subunit protein uS12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62266
#29: Protein 40S ribosomal protein S30 / / Small ribosomal subunit protein eS30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62861
#31: Protein 40S ribosomal protein S15a / / Small ribosomal subunit protein uS8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#32: Protein 40S ribosomal protein S8 / / Small ribosomal subunit protein eS8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62241
#33: Protein 40S ribosomal protein S24 / / Small ribosomal subunit protein eS24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62847
#34: Protein 40S ribosomal protein S5 / / Small ribosomal subunit protein uS7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46782
#35: Protein 40S ribosomal protein S16 / / Small ribosomal subunit protein uS9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62249
#36: Protein 40S ribosomal protein S3 / / Small ribosomal subunit protein uS3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#37: Protein 40S ribosomal protein S10 / / Small ribosomal subunit protein eS10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P46783
#38: Protein 40S ribosomal protein S15 / / RIG protein / Small ribosomal subunit protein uS19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62841
#40: Protein 40S ribosomal protein S19 / / Small ribosomal subunit protein eS19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39019
#41: Protein 40S ribosomal protein S25 / / Small ribosomal subunit protein eS25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62851
#42: Protein 40S ribosomal protein S18 / / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62269
#43: Protein 40S ribosomal protein S29 / / Small ribosomal subunit protein uS14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#45: Protein 40S ribosomal protein S12 / / Small ribosomal subunit protein eS12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#46: Protein 40S ribosomal protein S28 / / Small ribosomal subunit protein eS28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62857
#51: Protein 40S ribosomal protein S17 / / Small ribosomal subunit protein eS17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08708
#52: Protein 40S ribosomal protein S20 / / Small ribosomal subunit protein uS10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60866

+
RNA chain , 3 types, 3 molecules 7Aw

#22: RNA chain mRNA / Messenger RNA


Mass: 9172.806 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#24: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 603130.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#54: RNA chain Initiator Met-tRNA-i


Mass: 24231.510 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 174924

+
Protein/peptide , 1 types, 1 molecules 9

#23: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62945

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Protein , 3 types, 3 molecules ckj

#39: Protein Receptor of activated protein C kinase 1 / Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2- ...Cell proliferation-inducing gene 21 protein / Guanine nucleotide-binding protein subunit beta-2-like 1 / Guanine nucleotide-binding protein subunit beta-like protein 12.3 / Human lung cancer oncogene 7 protein / HLC-7 / Receptor for activated C kinase / Small ribosomal subunit protein RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P63244
#44: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62979
#56: Protein Eukaryotic initiation factor 4A-I / eIF4A-I / ATP-dependent RNA helicase eIF4A-1


Mass: 46207.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Production host: Escherichia coli (E. coli) / References: UniProt: P60842, RNA helicase

+
Non-polymers , 2 types, 91 molecules

#58: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#59: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 89 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
148S initiation complexRIBOSOME#1-#570MULTIPLE SOURCES
248S initiation complexCOMPLEX#22, #48-#50, #56-#571RECOMBINANT
348S initiation complexCOMPLEX#1-#21, #23-#47, #51-#551NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 1 sec. / Electron dose: 107 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37870 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 100.73 Å2
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063123668
ELECTRON MICROSCOPYf_angle_d1.1779176215
ELECTRON MICROSCOPYf_chiral_restr0.060321764
ELECTRON MICROSCOPYf_plane_restr0.007316082
ELECTRON MICROSCOPYf_dihedral_angle_d21.32550286

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