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- PDB-6g5i: Cryo-EM structure of a late human pre-40S ribosomal subunit - State R -

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Entry
Database: PDB / ID: 6g5i
TitleCryo-EM structure of a late human pre-40S ribosomal subunit - State R
Components
  • (40S ribosomal protein ...) x 30
  • (RNA-binding protein ...) x 2
  • 18S ribosomal RNA
  • Receptor of activated protein C kinase 1
  • Ribosomal protein S27aRibosome
  • Serine/threonine-protein kinase RIO1
KeywordsRIBOSOME / 40S / pre-40S / ribosome biogenesis
Function / homology
Function and homology information


methyltransferase complex / cleavage involved in rRNA processing / 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 / positive regulation of gastrulation / 5.8S rRNA binding / response to extracellular stimulus ...methyltransferase complex / cleavage involved in rRNA processing / 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 / positive regulation of gastrulation / 5.8S rRNA binding / response to extracellular stimulus / positive regulation of Golgi to plasma membrane protein transport / ubiquitin ligase inhibitor activity / negative regulation of RNA splicing / IRE1-RACK1-PP2A complex / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of protein homooligomerization / laminin receptor activity / regulation of cell division / signaling adaptor activity / negative regulation of ubiquitin protein ligase activity / negative regulation of endoplasmic reticulum unfolded protein response / negative regulation of DNA repair / response to TNF agonist / positive regulation of base-excision repair / positive regulation of DNA N-glycosylase activity / oxidized pyrimidine DNA binding / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of hydrogen peroxide-induced neuron death / positive regulation of ceramide biosynthetic process / NF-kappaB complex / mammalian oogenesis stage / erythrocyte homeostasis / negative regulation of phagocytosis / negative regulation of Wnt signaling pathway / positive regulation of endodeoxyribonuclease activity / regulation of establishment of cell polarity / pigmentation / protein kinase A binding / activation-induced cell death of T cells / cysteine-type endopeptidase activator activity involved in apoptotic process / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / supercoiled DNA binding / ubiquitin-like protein conjugating enzyme binding / positive regulation of mitochondrial depolarization / translation regulator activity / preribosome, small subunit precursor / rescue of stalled ribosome / phagocytic cup / ion channel inhibitor activity / positive regulation of cellular component movement / 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) / iron-sulfur cluster binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / fibroblast growth factor binding / stress granule assembly / positive regulation of T cell receptor signaling pathway / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / positive regulation of apoptotic signaling pathway / regulation of translational fidelity / maturation of SSU-rRNA / erythrocyte development / positive regulation of activated T cell proliferation / oxidized purine nucleobase lesion DNA N-glycosylase activity / monocyte chemotaxis / oxidized purine DNA binding / ribosomal small subunit export from nucleus / positive regulation of ubiquitin-protein transferase activity / positive regulation of cyclic-nucleotide phosphodiesterase activity / TOR signaling / negative regulation of protein kinase B signaling / small-subunit processome / regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of ubiquitin-dependent protein catabolic process / T cell proliferation involved in immune response / positive regulation of interleukin-2 production / spindle assembly / ribosomal small subunit biogenesis / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / positive regulation of JUN kinase activity / molecular adaptor activity / gastrulation / translation initiation factor binding / polysome / cellular response to interleukin-4 / positive regulation of microtubule polymerization / innate immune response in mucosa / viral transcription / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin binding / erythrocyte differentiation / mitotic cell cycle checkpoint / polysomal ribosome / positive regulation of cell cycle / tubulin binding / Hsp70 protein binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of peptidyl-serine phosphorylation
Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S13 / Ribosomal protein S21e / Ribosomal S17 / Ribosomal protein S9/S16 / Ribosomal protein S19 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S15 ...Ribosomal protein S3, C-terminal domain superfamily / Ribosomal protein S13 / Ribosomal protein S21e / Ribosomal S17 / Ribosomal protein S9/S16 / Ribosomal protein S19 / Ribosomal protein S11 / Ribosomal protein S4/S9, N-terminal / Ribosomal S13/S15 N-terminal domain / Ribosomal protein S15 / Ribosomal protein S2 / Ribosomal protein S24e / Ribosomal protein S10 / WD40 repeat / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / Ribosomal protein S3Ae / Ribosomal protein S6e / Ribosomal protein S3, C-terminal / Ribosomal protein S19e / Ribosomal protein S17e / Ribosomal_S17 N-terminal / Ribosomal protein S11 / Ribosomal protein S13/S18 / Ribosomal protein S14 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein S30 / Ribosomal protein S5, C-terminal / Ribosomal protein S25 / K Homology domain / K Homology domain, type 2 / Ribosomal protein S14p/S29e / Ribosomal protein S28e / Ribosomal protein S27 / S25 ribosomal protein / Ribosomal protein S19/S15 / RNA-binding S4 domain / Ribosomal protein S27a / Ribosomal protein S24e / Ribosomal protein S12/S23 / Ribosomal protein S8 / PIN domain / Ribosomal protein S21e / Ribosomal protein S10p/S20e / Ribosomal protein S19e / Ribosomal protein S17 / Ribosomal protein S8e / RS4NT (NUC023) domain / Ribosomal S3Ae family / S27a-like superfamily / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / RNA-binding protein NOB1 / Pre-rRNA-processing protein PNO1-like / Ribosomal protein S4, KOW domain / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S2 / 40S ribosomal protein SA C-terminus / K Homology domain, type 1 superfamily / Ribosomal protein S21e superfamily / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal domain / Ribosomal protein S3, C-terminal domain / KH domain / KOW motif / Ribosomal protein S6e / Ribosomal family S4e / S4 domain / Ribosomal protein S7p/S5e / Ribosomal protein S7e / Ribosomal protein S4e, central domain superfamily / Ribosomal protein S4e / Ribosomal protein S28e / Ribosomal protein S5 / Ribosomal protein S9 / RIO kinase / Ribosomal protein S8 / Ubiquitin-like domain / Ribosomal protein S27e / Ribosomal protein S15 / Ribosomal protein S7e / Ribosomal protein S12e / Plectin/S10 domain / Ribosomal protein S19e domain superfamily / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S17/S11 / Ribosomal protein S8e / Ribosomal protein S5/S7 / Ribosomal protein S7 domain superfamily / Ribosomal protein S10 domain superfamily / Ribosomal protein S11 superfamily / RNA-binding S4 domain superfamily / 40S Ribosomal protein S10 / Ubiquitin family / Plectin/S10, N-terminal / Ribosomal protein S27a / Ribosomal protein S17, conserved site / Ribosomal protein S15P / Ribosomal protein S4/S9 / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S19 conserved site / Ribosomal protein S7, conserved site
40S ribosomal protein S17 / 40S ribosomal protein S28 / 40S ribosomal protein SA / gb:151415227: / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 40S ribosomal protein S24 / 40S ribosomal protein S25 ...40S ribosomal protein S17 / 40S ribosomal protein S28 / 40S ribosomal protein SA / gb:151415227: / 40S ribosomal protein S11 / 40S ribosomal protein S4, X isoform / 40S ribosomal protein S6 / 40S ribosomal protein S15 / 40S ribosomal protein S24 / 40S ribosomal protein S25 / RNA-binding protein NOB1 / 40S ribosomal protein S29 / RNA-binding protein PNO1 / Serine/threonine-protein kinase RIO1 / Ribosomal protein S27a / Receptor of activated protein C kinase 1 / 40S ribosomal protein S21 / Ubiquitin-40S ribosomal protein S27a / 40S ribosomal protein S13 / 40S ribosomal protein S18 / 40S ribosomal protein S2 / 40S ribosomal protein S10 / 40S ribosomal protein S3 / 40S ribosomal protein S12 / 40S ribosomal protein S19 / 40S ribosomal protein S27 / 40S ribosomal protein S9 / 40S ribosomal protein S30 / 40S ribosomal protein S20 / 40S ribosomal protein S23 / 40S ribosomal protein S3a / 40S ribosomal protein S7 / 40S ribosomal protein S8 / 40S ribosomal protein S15a / 40S ribosomal protein S16 / 40S ribosomal protein S14 / 40S ribosomal protein S5
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 29, 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 1.3Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][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: 18S ribosomal RNA
A: 40S ribosomal protein SA
B: 40S ribosomal protein S3a
C: 40S ribosomal protein S2
D: 40S ribosomal protein S3
E: 40S ribosomal protein S4, X isoform
F: 40S ribosomal protein S5
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
K: 40S ribosomal protein S10
L: 40S ribosomal protein S11
M: 40S ribosomal protein S12
N: 40S ribosomal protein S13
O: 40S ribosomal protein S14
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
U: 40S ribosomal protein S20
V: 40S ribosomal protein S21
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: 40S ribosomal protein S24
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: Ribosomal protein S27a
g: Receptor of activated protein C kinase 1
x: RNA-binding protein PNO1
y: RNA-binding protein NOB1
z: Serine/threonine-protein kinase RIO1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,353,76139
Polymers1,353,56536
Non-polymers1963
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area201350 Å2
ΔGint-1440 kcal/mol
Surface area417600 Å2
MethodPISA

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Components

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40S ribosomal protein ... , 30 types, 30 molecules ABCDEFGHIJKLMNOPQRSTUVWXYZbcde

#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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / References: UniProt: P15880
#5: 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) / Cell line: HEK293
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#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) / Cell line: HEK293 / References: UniProt: P62701
#7: 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) / Cell line: HEK293 / References: UniProt: P46782
#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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / References: UniProt: P46781
#12: 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) / Cell line: HEK293 / References: UniProt: P46783
#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) / Cell line: HEK293 / References: UniProt: P62280
#14: 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) / Cell line: HEK293 / References: UniProt: P25398
#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) / Cell line: HEK293 / 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) / Cell line: HEK293 / References: UniProt: P62263
#17: 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) / Cell line: HEK293 / References: UniProt: P62841
#18: 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) / Cell line: HEK293 / References: UniProt: P62249
#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) / Cell line: HEK293 / References: UniProt: P08708
#20: 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) / Cell line: HEK293 / References: UniProt: P62269
#21: 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) / Cell line: HEK293 / References: UniProt: P39019
#22: 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) / Cell line: HEK293 / References: UniProt: P60866
#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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / 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) / Cell line: HEK293 / References: UniProt: P62847
#27: 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) / Cell line: HEK293 / References: UniProt: P62851
#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) / Cell line: HEK293 / References: UniProt: P42677
#29: 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) / Cell line: HEK293 / References: UniProt: P62857
#30: 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) / Cell line: HEK293 / References: UniProt: P62273
#31: 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) / Cell line: HEK293 / References: UniProt: P62861

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Protein , 3 types, 3 molecules fgz

#32: Protein Ribosomal protein S27a / Ribosome


Mass: 17944.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q5RKT7, UniProt: P62979*PLUS
#33: 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) / Cell line: HEK293 / References: UniProt: P63244
#36: Protein Serine/threonine-protein kinase RIO1 / RIO kinase 1


Mass: 65692.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RIOK1 / Production host: Escherichia coli K-12 (bacteria)
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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RNA-binding protein ... , 2 types, 2 molecules xy

#34: Protein RNA-binding protein PNO1


Mass: 27970.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PNO1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9NRX1
#35: 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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOB1, ART4, NOB1P, PSMD8BP1, MSTP158 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9ULX3

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RNA chain / Non-polymers , 2 types, 4 molecules 2

#1: RNA chain 18S ribosomal RNA /


Mass: 607057.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: GenBank: 151415227
#37: Chemical ChemComp-ZN / ZINC ION / Zinc


Mass: 65.409 Da / Num. of mol.: 3 / 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 late human pre-40S ribosomal subunit - State R
Type: RIBOSOME
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36
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: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83883 / Symmetry type: POINT

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