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- PDB-6zxh: Cryo-EM structure of a late human pre-40S ribosomal subunit - State H2 -

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Entry
Database: PDB / ID: 6zxh
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - State H2
Components
  • (40S ribosomal protein ...) x 31
  • Probable RNA-binding protein EIF1AD
  • Receptor of activated protein C kinase 1
  • Serine/threonine-protein kinase RIO1
  • Ubiquitin-40S ribosomal protein S27a
  • pre-18S ribosomal RNA
KeywordsRIBOSOME / Ribosome Biogenesis / Pre-40S
Function / homology
Function and homology information


methyltransferase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / positive regulation of rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / mammalian oogenesis stage / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus ...methyltransferase complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / positive regulation of rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / mammalian oogenesis stage / positive regulation of gastrulation / positive regulation of Golgi to plasma membrane protein transport / response to extracellular stimulus / negative regulation of RNA splicing / IRE1-RACK1-PP2A 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 / negative regulation of hydrogen peroxide-induced neuron death / response to TNF agonist / positive regulation of base-excision repair / negative regulation of DNA repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of ubiquitin protein ligase activity / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of ceramide biosynthetic process / erythrocyte homeostasis / NF-kappaB complex / negative regulation of phagocytosis / regulation of establishment of cell polarity / intermediate filament cytoskeleton / positive regulation of endodeoxyribonuclease activity / signaling adaptor activity / oxidized purine DNA binding / negative regulation of Wnt signaling pathway / 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 / preribosome, small subunit precursor / 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 / positive regulation of T cell receptor signaling pathway / poly(U) RNA binding / stress granule assembly / monocyte chemotaxis / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / T cell proliferation involved in immune response / positive regulation of ubiquitin-protein transferase activity / BH3 domain binding / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of activated T cell proliferation / GABA-ergic synapse / positive regulation of cyclic-nucleotide phosphodiesterase activity / ribosomal small subunit export from nucleus / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / regulation of translational fidelity / gastrulation / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein kinase B signaling / spindle assembly / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / positive regulation of JUN kinase activity / SRP-dependent cotranslational protein targeting to membrane / ribosomal small subunit biogenesis / translation initiation factor binding / positive regulation of DNA repair / molecular adaptor activity / polysome / positive regulation of microtubule polymerization / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin binding / positive regulation of cell cycle / endoplasmic reticulum mannose trimming / negative regulation of peptidyl-serine phosphorylation / Hsp70 protein binding / cytoplasmic pattern recognition receptor signaling pathway / translation initiation factor activity / tubulin binding / erythrocyte differentiation / innate immune response in mucosa / positive regulation of intrinsic apoptotic signaling pathway
Translation initiation factor 1A / IF-1 / Ribosomal protein S3, C-terminal / Ubiquitin-like domain / Ribosomal protein S8 / RIO kinase / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S4e / Ribosomal protein S26e / Ribosomal protein S8e ...Translation initiation factor 1A / IF-1 / Ribosomal protein S3, C-terminal / Ubiquitin-like domain / Ribosomal protein S8 / RIO kinase / Ribosomal protein S9 / Ribosomal protein S5 / Ribosomal protein S4e / Ribosomal protein S26e / Ribosomal protein S8e / Ribosomal protein S14 / Ribosomal protein S17e / Translation initiation factor 1A (eIF-1A) / Ribosomal protein S19e / Ribosomal protein S6e / Ribosomal protein S15 / Ribosomal protein S3Ae / WD40 repeat / Ribosomal protein S10 / Ribosomal protein S2 / Ribosomal protein S13 / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S21e / Ribosomal protein S11 / Ribosomal protein S24e / Ribosomal protein S19/S15 / Ribosomal protein S27a / RNA-binding S4 domain / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S27 / Ribosomal protein S7e / Ribosomal protein S25 / 40S ribosomal protein S11, N-terminal / in:ipr038111: / 40S Ribosomal protein S10 / RNA-binding S4 domain superfamily / Ribosomal protein S11 superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S7 domain superfamily / Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S17e-like superfamily / Winged helix DNA-binding domain superfamily / Ribosomal protein S7 domain / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / Ribosomal protein S8 superfamily / 40S ribosomal protein SA, C-terminal domain / Ribosomal protein S12e / 40S ribosomal protein S4, C-terminal domain / Ubiquitin-like domain superfamily / 50S ribosomal protein L30e-like / Ribosomal protein S28e conserved site / Ribosomal protein S17, archaeal/eukaryotic / 40S ribosomal protein SA / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S2, eukaryotic / Ribosomal protein S10 domain / 30s ribosomal protein S13, C-terminal / Ribosomal protein S5/S7 / Ribosomal protein S17/S11 / Ribosomal protein S28e / K Homology domain, type 2 / Ribosomal protein S5, C-terminal / Ribosomal protein S26e superfamily / Ribosomal protein S8e, conserved site / Ribosomal S11, conserved site / Ribosomal protein S2, conserved site / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S10, conserved site / Ribosomal protein S13, conserved site / Ribosomal protein S14, conserved site / Ribosomal protein S17e, conserved site / Ribosomal protein S19e, conserved site / Ribosomal protein S21e, conserved site / Ribosomal protein S3, conserved site / Ribosomal protein S3Ae, conserved site / Ribosomal protein S6e, conserved site / RIO kinase, conserved site / Ribosomal protein S4, conserved site / WD40 repeat, conserved site / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S17, conserved site / G-protein beta WD-40 repeat / Ribosomal protein S5 domain 2-type fold / Ribosomal protein S9, conserved site / Ribosomal protein S7, conserved site / Ribosomal protein S19 conserved site / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S4/S9 / Ribosomal protein S15P / Ribosomal protein S19/S15, superfamily / Ribosomal S24e conserved site / WD40-repeat-containing domain / Plectin/S10, N-terminal / S15/NS1, RNA-binding / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal
40S ribosomal protein S21 / Serine/threonine-protein kinase RIO1 / 40S ribosomal protein S15a / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 40S ribosomal protein S27 ...40S ribosomal protein S21 / Serine/threonine-protein kinase RIO1 / 40S ribosomal protein S15a / 40S ribosomal protein S17 / 40S ribosomal protein SA / 40S ribosomal protein S2 / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 40S ribosomal protein S27 / 40S ribosomal protein S9 / 40S ribosomal protein S5 / 40S ribosomal protein S10 / 40S ribosomal protein S20 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 40S ribosomal protein S16 / Probable RNA-binding protein EIF1AD / 40S ribosomal protein S24 / Receptor of activated protein C kinase 1 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S30 / 40S ribosomal protein S28 / 40S ribosomal protein S26 / 40S ribosomal protein S25 / 40S ribosomal protein S15 / 40S ribosomal protein S14 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S11 / 40S ribosomal protein S13 / 40S ribosomal protein S29 / 40S ribosomal protein S23 / 40S ribosomal protein S18
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsAmeismeier, M. / Zemp, I. / van den Heuvel, J. / Thoms, M. / Berninghausen, O. / Kutay, U. / Beckmann, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK1721 Germany
CitationJournal: Nature / Year: 2020
Title: Structural basis for the final steps of human 40S ribosome maturation.
Authors: Michael Ameismeier / Ivo Zemp / Jasmin van den Heuvel / Matthias Thoms / Otto Berninghausen / Ulrike Kutay / Roland Beckmann /
Abstract: Eukaryotic ribosomes consist of a small 40S and a large 60S subunit that are assembled in a highly coordinated manner. More than 200 factors ensure correct modification, processing and folding of ...Eukaryotic ribosomes consist of a small 40S and a large 60S subunit that are assembled in a highly coordinated manner. More than 200 factors ensure correct modification, processing and folding of ribosomal RNA and the timely incorporation of ribosomal proteins. Small subunit maturation ends in the cytosol, when the final rRNA precursor, 18S-E, is cleaved at site 3 by the endonuclease NOB1. Previous structures of human 40S precursors have shown that NOB1 is kept in an inactive state by its partner PNO1. The final maturation events, including the activation of NOB1 for the decisive rRNA-cleavage step and the mechanisms driving the dissociation of the last biogenesis factors have, however, remained unresolved. Here we report five cryo-electron microscopy structures of human 40S subunit precursors, which describe the compositional and conformational progression during the final steps of 40S assembly. Our structures explain the central role of RIOK1 in the displacement and dissociation of PNO1, which in turn allows conformational changes and activation of the endonuclease NOB1. In addition, we observe two factors, eukaryotic translation initiation factor 1A domain-containing protein (EIF1AD) and leucine-rich repeat-containing protein 47 (LRRC47), which bind to late pre-40S particles near RIOK1 and the central rRNA helix 44. Finally, functional data shows that EIF1AD is required for efficient assembly factor recycling and 18S-E processing. Our results thus enable a detailed understanding of the last steps in 40S formation in human cells and, in addition, provide evidence for principal differences in small ribosomal subunit formation between humans and the model organism Saccharomyces cerevisiae.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
2: pre-18S ribosomal RNA
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
h: 40S ribosomal protein S26
E: 40S ribosomal protein S4, X isoform
D: 40S ribosomal protein S3
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
F: 40S ribosomal protein S5
L: 40S ribosomal protein S11
K: 40S ribosomal protein S10
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
M: 40S ribosomal protein S12
P: 40S ribosomal protein S15
R: 40S ribosomal protein S17
Q: 40S ribosomal protein S16
S: 40S ribosomal protein S18
T: 40S ribosomal protein S19
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
U: 40S ribosomal protein S20
Z: 40S ribosomal protein S25
b: 40S ribosomal protein S27
c: 40S ribosomal protein S28
d: 40S ribosomal protein S29
e: 40S ribosomal protein S30
f: Ubiquitin-40S ribosomal protein S27a
g: Receptor of activated protein C kinase 1
j: Probable RNA-binding protein EIF1AD
z: Serine/threonine-protein kinase RIO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,311,526172
Polymers1,307,50536
Non-polymers4,020136
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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RNA chain , 1 types, 1 molecules 2

#1: RNA chain pre-18S ribosomal RNA


Mass: 603524.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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

#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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

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Protein , 4 types, 4 molecules fgjz

#33: 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
#34: 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
#35: Protein Probable RNA-binding protein EIF1AD / Eukaryotic translation initiation factor 1A domain-containing protein / Haponin


Mass: 19081.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q8N9N8
#36: Protein Serine/threonine-protein kinase RIO1 / RIO kinase 1


Mass: 65692.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9BRS2, non-specific serine/threonine protein kinase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Non-polymers , 4 types, 136 molecules

#37: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#38: Chemical...
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 131 / Source method: obtained synthetically / Formula: Mg
#39: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#40: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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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

ComponentName: Cryo-EM structure of a late human pre-40S ribosomal subunit - State H2
Type: RIBOSOME / Details: Map filtered at local resolution / Entity ID: #1-#36 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human) / Strain: HEK293T
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144738 / Symmetry type: POINT

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