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- PDB-6g18: Cryo-EM structure of a late human pre-40S ribosomal subunit - State C -

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Basic information

Entry
Database: PDB / ID: 6g18
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - State C
Components
  • (40S ribosomal protein ...) x 26
  • (RNA-binding protein ...) x 2
  • Bystin
  • Pre-rRNA-processing protein TSR1 homolog
  • Protein LTV1 homolog
  • Receptor of activated protein C kinase 1
  • Serine/threonine-protein kinase RIO2
  • Ubiquitin-40S ribosomal protein S27a
  • pre-18S ribosomal RNA
KeywordsRIBOSOME / 40S / pre-40S / ribosome biogenesis
Function / homology
Function and homology information


positive regulation of ribosomal small subunit export from nucleus / regulation of protein localization to nucleolus / cleavage involved in rRNA processing / positive regulation of rRNA processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation ...positive regulation of ribosomal small subunit export from nucleus / regulation of protein localization to nucleolus / cleavage involved in rRNA processing / positive regulation of rRNA processing / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / protein tyrosine kinase inhibitor activity / positive regulation of gastrulation / regulation of mitotic metaphase/anaphase transition / 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 / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of hydrogen peroxide-induced neuron death / negative regulation of ubiquitin protein ligase activity / positive regulation of ceramide biosynthetic process / U3 snoRNA binding / erythrocyte homeostasis / mammalian oogenesis stage / negative regulation of phagocytosis / regulation of establishment of cell polarity / signaling adaptor activity / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of Wnt signaling pathway / protein targeting to peroxisome / activation-induced cell death of T cells / positive regulation of mitochondrial depolarization / 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 cellular component movement / fibroblast growth factor binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / rescue of stalled ribosome / snoRNA binding / poly(U) RNA binding / stress granule assembly / monocyte chemotaxis / 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) / GABA-ergic synapse / erythrocyte development / positive regulation of cyclic-nucleotide phosphodiesterase activity / TOR signaling / ribosomal small subunit export from nucleus / regulation of tumor necrosis factor-mediated signaling pathway / maturation of SSU-rRNA / regulation of translational fidelity / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein kinase B signaling / T cell proliferation involved in immune response / negative regulation of ubiquitin-dependent protein catabolic process / small-subunit processome / SRP-dependent cotranslational protein targeting to membrane / ribosomal small subunit biogenesis / gastrulation / translation initiation factor binding / molecular adaptor activity / polysome / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin binding / positive regulation of cell cycle / visual perception / negative regulation of peptidyl-serine phosphorylation / erythrocyte differentiation / innate immune response in mucosa / positive regulation of intrinsic apoptotic signaling pathway / polysomal ribosome / endoribonuclease activity / SH2 domain binding / translational initiation / MyD88-independent toll-like receptor signaling pathway / mRNA 3'-UTR binding / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / cyclin binding / osteoblast differentiation / nucleotide-excision repair, DNA damage recognition / maintenance of translational fidelity / positive regulation of translational fidelity / TRIF-dependent toll-like receptor signaling pathway / nucleotide-excision repair, DNA duplex unwinding / presynapse / protein kinase C binding / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / rough endoplasmic reticulum / cellular response to glucose stimulus / intracellular transport of virus
Ribosomal S3Ae family / K Homology domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S5, C-terminal / Putative WW-binding domain and destruction box / Ribosomal protein S25 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 ...Ribosomal S3Ae family / K Homology domain / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S5, C-terminal / Putative WW-binding domain and destruction box / Ribosomal protein S25 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / PIN domain of ribonuclease / RNA-binding S4 domain / Nin one binding (NOB1) Zn-ribbon like / Bystin / Ribosomal protein S27a / PIN domain / Ribosomal protein S19/S15 / Ribosomal protein S24e / Ribosomal protein S11 / Ribosomal protein S19A/S15e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S4/S9, N-terminal / Nucleic acid-binding, OB-fold / Ribosomal protein S24e / Ribosomal protein S6, eukaryotic / Ribosomal protein S4e, central region / Ribosomal protein S4e, N-terminal / Ribosomal protein S5, N-terminal / AARP2CN / Ribosomal protein L23/L15e core domain superfamily / Ribosomal protein S13/S15, N-terminal / Zinc-binding ribosomal protein / KOW / Protein kinase-like domain superfamily / Ribosomal protein S13-like, H2TH / S15/NS1, RNA-binding / Bystin / Low temperature viability protein Ltv1 / Ribosome biogenesis protein BMS1/TSR1, C-terminal / Ribosomal protein S30 / Ribosomal protein S12/S23 / Ribosomal protein S21e / Ribosomal protein S13 / Nin one binding (NOB1) Zn-ribbon-like / Ribosomal protein S30 / Ribosomal protein S17 / Ribosomal_S17 N-terminal / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S15 / Ribosomal protein S27a / Ubiquitin family / Ribosomal protein S11 / Ribosomal protein S28e / Ribosomal protein S5/S7 / Ribosomal protein S27 / Ribosomal protein S9/S16 / S25 ribosomal protein / Ribosomal S17 / 40S ribosomal protein SA C-terminus / Ribosomal protein S13/S18 / Ribosomal protein S21e / Ribosomal protein S8 / S4 domain / Ribosomal protein S17/S11 / Ribosomal protein S2 / Ribosomal protein S5 / WD40 repeat / Ribosomal protein S3Ae / 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal / Ribosomal protein S6e / Ribosomal protein S19e / Ribosomal protein S17e / Ribosomal protein S8e / Ribosomal protein S4e / Ribosomal protein S9 / Ribosomal protein S28e / Low temperature viability protein / RIO kinase / Ribosomal protein S8 / Ubiquitin-like domain / Ribosomal protein S27 / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S12e / Ribosomal protein L2, domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / RIO2 kinase winged helix domain, N-terminal / Ribonuclease, PIN domain / Ribosomal protein S17e-like superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40-repeat-containing domain superfamily / NOB1 zinc finger-like superfamily / Ribosomal protein S8 superfamily / Putative WW-binding domain and destruction box / 40S ribosomal protein S11, N-terminal / Ribosomal protein S7 domain superfamily / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein S4, C-terminal domain / Serine/threonine-protein kinase Rio2
Bystin / 40S ribosomal protein S11 / 40S ribosomal protein S12 / 40S ribosomal protein S2 / 40S ribosomal protein SA / 40S ribosomal protein S15 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S17 / 40S ribosomal protein S25 ...Bystin / 40S ribosomal protein S11 / 40S ribosomal protein S12 / 40S ribosomal protein S2 / 40S ribosomal protein SA / 40S ribosomal protein S15 / 40S ribosomal protein S6 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S17 / 40S ribosomal protein S25 / 40S ribosomal protein S13 / 40S ribosomal protein S18 / 40S ribosomal protein S15a / 40S ribosomal protein S23 / 40S ribosomal protein S14 / 40S ribosomal protein S16 / 40S ribosomal protein S24 / 40S ribosomal protein S28 / Pre-rRNA-processing protein TSR1 homolog / RNA-binding protein NOB1 / Receptor of activated protein C kinase 1 / 40S ribosomal protein S21 / Ubiquitin-40S ribosomal protein S27a / Protein LTV1 homolog / Serine/threonine-protein kinase RIO2 / RNA-binding protein PNO1 / gb:151415227: / 40S ribosomal protein S19 / 40S ribosomal protein S7 / 40S ribosomal protein S30 / 40S ribosomal protein S3a / 40S ribosomal protein S5 / 40S ribosomal protein S9 / 40S ribosomal protein S27 / 40S ribosomal protein S8
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsAmeismeier, M. / Cheng, J. / Berninghausen, O. / Beckmann, R.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationSFB646 Germany
German Research FoundationGRK1721 Germany
German Research FoundationFOR1805 Germany
European Research CouncilCRYOTRANSLATION Germany
CitationJournal: Nature / Year: 2018
Title: Visualizing late states of human 40S ribosomal subunit maturation.
Authors: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann /
Abstract: The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high- ...The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 17, 2018Group: Data collection / Refinement description / Category: refine
Revision 1.4Oct 30, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.5Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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Assembly

Deposited unit
2: pre-18S ribosomal RNA
F: 40S ribosomal protein S5
M: 40S ribosomal protein S12
P: 40S ribosomal protein S15
Q: 40S ribosomal protein S16
R: 40S ribosomal protein S17
S: 40S ribosomal protein S18
T: 40S ribosomal protein S19
Z: 40S ribosomal protein S25
c: 40S ribosomal protein S28
f: Ubiquitin-40S ribosomal protein S27a
g: Receptor of activated protein C kinase 1
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
E: 40S ribosomal protein S4, X isoform
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
L: 40S ribosomal protein S11
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
b: 40S ribosomal protein S27
e: 40S ribosomal protein S30
x: RNA-binding protein PNO1
y: RNA-binding protein NOB1
u: Pre-rRNA-processing protein TSR1 homolog
w: Bystin
v: Serine/threonine-protein kinase RIO2
t: Protein LTV1 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,479,28937
Polymers1,479,15835
Non-polymers1312
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area208420 Å2
ΔGint-1516 kcal/mol
Surface area449000 Å2
MethodPISA

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Components

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40S ribosomal protein ... , 26 types, 26 molecules FMPQRSTZcABCEGHIJLNOVWXYbe

#2: 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
#3: 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
#4: 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
#5: 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
#6: 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
#7: 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
#8: 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
#9: 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
#10: 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
#13: 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
#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 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#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

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Protein , 6 types, 6 molecules fguwvt

#11: 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
#12: 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
#32: Protein Pre-rRNA-processing protein TSR1 homolog


Mass: 91951.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q2NL82
#33: Protein Bystin


Mass: 49673.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13895
#34: Protein Serine/threonine-protein kinase RIO2 / RIO kinase 2


Mass: 63372.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
References: UniProt: Q9BVS4, non-specific serine/threonine protein kinase
#35: Protein Protein LTV1 homolog


Mass: 54935.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96GA3

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RNA-binding protein ... , 2 types, 2 molecules xy

#30: Protein RNA-binding protein PNO1


Mass: 27970.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRX1
#31: Protein RNA-binding protein NOB1 / Phosphorylation regulatory protein HP-10 / Protein ART-4


Mass: 46743.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9ULX3

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RNA chain / Non-polymers , 2 types, 3 molecules 2

#1: RNA chain pre-18S ribosomal RNA


Mass: 604102.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 151415227
#36: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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 human pre-40S ribosomal subunit with bound PNO1, NOB1, TSR1, BYST, RIOK2 and LTV1
Type: RIBOSOME
Details: Cytoplasmic precursor of the human small ribosomal subunit (pre-40S) purified by affinity chromatography using the StFLAG-tagged ribosomal biogenesis factor PNO1
Entity ID: #1-#35 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
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: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 287847 / Symmetry type: POINT
RefinementResolution: 3.6→260.16 Å / Cor.coef. Fo:Fc: 0.919 / ESU R: 0.622
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.27846 --
Obs0.27846 553304 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 104.814 Å2
Baniso -1Baniso -2Baniso -3
1--2.98 Å2-3.27 Å20.42 Å2
2--3.68 Å2-3.71 Å2
3----0.71 Å2
Refinement stepCycle: 1 / Total: 83825
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01688874
ELECTRON MICROSCOPYr_bond_other_d00.0264628
ELECTRON MICROSCOPYr_angle_refined_deg1.1091.637127919
ELECTRON MICROSCOPYr_angle_other_deg3.4253151427
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.21556014
ELECTRON MICROSCOPYr_dihedral_angle_2_deg39.14822.6362162
ELECTRON MICROSCOPYr_dihedral_angle_3_deg19.337159491
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.3415498
ELECTRON MICROSCOPYr_chiral_restr0.0860.213989
ELECTRON MICROSCOPYr_gen_planes_refined0.0050.0273225
ELECTRON MICROSCOPYr_gen_planes_other0.0060.0218985
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.22710.63324194
ELECTRON MICROSCOPYr_mcbond_other5.22710.63324193
ELECTRON MICROSCOPYr_mcangle_it9.42615.92430162
ELECTRON MICROSCOPYr_mcangle_other9.42615.92430163
ELECTRON MICROSCOPYr_scbond_it5.03610.74664680
ELECTRON MICROSCOPYr_scbond_other5.03610.74664681
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other8.83915.93297758
ELECTRON MICROSCOPYr_long_range_B_refined14.42199593
ELECTRON MICROSCOPYr_long_range_B_other14.42199594
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.502 40797 -
Rfree-0 -
Obs--100 %

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