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- PDB-7tql: CryoEM structure of the human 40S small ribosomal subunit in comp... -

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Basic information

Entry
Database: PDB / ID: 7tql
TitleCryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.
Components
  • (40S ribosomal protein ...) x 19
  • (ribosomal protein ...) x 12
  • 18S ribosomal RNA
  • Eukaryotic translation initiation factor 5B
  • Human Met-tRNAiMet
  • Isoform 3 of 40S ribosomal protein S24
  • Receptor of activated protein C kinase 1
  • Translation initiation factor eIF1A
KeywordsRIBOSOME / eIF5B / translation / initiation / eIF1A
Function / homology
Function and homology information


negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / IRE1-RACK1-PP2A complex ...negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / protein tyrosine kinase inhibitor activity / positive regulation of endodeoxyribonuclease activity / IRE1-RACK1-PP2A complex / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / protein-synthesizing GTPase / supercoiled DNA binding / neural crest cell differentiation / regulation of translational initiation / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / positive regulation of ubiquitin-protein transferase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / regulation of establishment of cell polarity / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / Formation of the ternary complex, and subsequently, the 43S complex / cytoplasmic side of rough endoplasmic reticulum membrane / negative regulation of ubiquitin protein ligase activity / protein kinase A binding / ion channel inhibitor activity / Ribosomal scanning and start codon recognition / pigmentation / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / monocyte chemotaxis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / TOR signaling / Protein hydroxylation / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / positive regulation of GTPase activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / protein serine/threonine kinase inhibitor activity / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / phagocytic cup / regulation of translational fidelity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of protein binding / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / positive regulation of intrinsic apoptotic signaling pathway / spindle assembly / rough endoplasmic reticulum / 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) / translation regulator activity / ribosomal small subunit export from nucleus / positive regulation of cell cycle / gastrulation / translation initiation factor binding / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / DNA-(apurinic or apyrimidinic site) endonuclease activity / Maturation of protein E / Maturation of protein E / signaling adaptor activity / MDM2/MDM4 family protein binding / translation initiation factor activity / positive regulation of microtubule polymerization / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / negative regulation of protein ubiquitination
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / K homology (KH) domain ...Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / 30s Ribosomal Protein S19; Chain A / Ribosomal protein S19/S15 / K homology (KH) domain / Helicase, Ruva Protein; domain 3 - #50 / Double Stranded RNA Binding Domain - #20 / Translation factors / GMP Synthetase; Chain A, domain 3 / Double Stranded RNA Binding Domain / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S5, eukaryotic/archaeal / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / S27a-like superfamily / 40S Ribosomal protein S10 / Plectin/S10, N-terminal / Plectin/S10 domain / : / Ribosomal protein S7e signature. / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S3, eukaryotic/archaeal / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Elongation Factor Tu (Ef-tu); domain 3 / Ribosomal protein S27e signature. / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S19e / Ribosomal protein S19e / Ribosomal_S19e / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S11, N-terminal / Ribosomal_S17 N-terminal / : / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S4e, N-terminal / RS4NT (NUC023) domain / Ribosomal protein S4, KOW domain / Ribosomal protein S4e / Ribosomal protein S4e, central region / Ribosomal protein S4e, central domain superfamily / Ribosomal family S4e / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Helicase, Ruva Protein; domain 3 / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S8e / Ribosomal protein S6e / Ribosomal protein S5/S7, eukaryotic/archaeal / Ribosomal protein S6e / Ribosomal protein S6e / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein S4/S9, eukaryotic/archaeal / Ribosomal protein S8e/ribosomal biogenesis NSA2 / Ribosomal protein S8e / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ribosomal protein S3, conserved site / Ribosomal protein S3 signature. / KH domain / Type-2 KH domain profile. / K Homology domain, type 2 / Ribosomal protein S3, C-terminal / Ribosomal protein S3, C-terminal domain
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10 / Eukaryotic translation initiation factor 5B / Small ribosomal subunit protein uS5 ...GUANOSINE-5'-MONOPHOSPHATE / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS10 / Eukaryotic translation initiation factor 5B / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS17 / Small ribosomal subunit protein eS4, X isoform / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein eS24 / Small ribosomal subunit protein eS26 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLapointe, C.P. / Grosely, R. / Sokabe, M. / Alvarado, C. / Wang, J. / Montabana, E. / Villa, N. / Shin, B. / Dever, T. / Fraser, C. ...Lapointe, C.P. / Grosely, R. / Sokabe, M. / Alvarado, C. / Wang, J. / Montabana, E. / Villa, N. / Shin, B. / Dever, T. / Fraser, C. / Fernandez, I.S. / Puglisi, J.D.
Funding support United States, Sweden, 3items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRG-#2321-18 United States
Knut and Alice Wallenberg Foundation(KAW2015.0406 Sweden
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)(GM011378 United States
CitationJournal: Nature / Year: 2022
Title: eIF5B and eIF1A reorient initiator tRNA to allow ribosomal subunit joining.
Authors: Christopher P Lapointe / Rosslyn Grosely / Masaaki Sokabe / Carlos Alvarado / Jinfan Wang / Elizabeth Montabana / Nancy Villa / Byung-Sik Shin / Thomas E Dever / Christopher S Fraser / ...Authors: Christopher P Lapointe / Rosslyn Grosely / Masaaki Sokabe / Carlos Alvarado / Jinfan Wang / Elizabeth Montabana / Nancy Villa / Byung-Sik Shin / Thomas E Dever / Christopher S Fraser / Israel S Fernández / Joseph D Puglisi /
Abstract: Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases. A key commitment step is when the ribosomal subunits join at a ...Translation initiation defines the identity and quantity of a synthesized protein. The process is dysregulated in many human diseases. A key commitment step is when the ribosomal subunits join at a translation start site on a messenger RNA to form a functional ribosome. Here, we combined single-molecule spectroscopy and structural methods using an in vitro reconstituted system to examine how the human ribosomal subunits join. Single-molecule fluorescence revealed when the universally conserved eukaryotic initiation factors eIF1A and eIF5B associate with and depart from initiation complexes. Guided by single-molecule dynamics, we visualized initiation complexes that contained both eIF1A and eIF5B using single-particle cryo-electron microscopy. The resulting structure revealed how eukaryote-specific contacts between the two proteins remodel the initiation complex to orient the initiator aminoacyl-tRNA in a conformation compatible with ribosomal subunit joining. Collectively, our findings provide a quantitative and architectural framework for the molecular choreography orchestrated by eIF1A and eIF5B during translation initiation in humans.
History
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Dec 14, 2022Group: Refinement description / Category: refine / Item: _refine.ls_d_res_high
Revision 1.4Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Eukaryotic translation initiation factor 5B
2: 18S ribosomal RNA
3: Human Met-tRNAiMet
4: Translation initiation factor eIF1A
B: ribosomal protein uS2
C: ribosomal protein uS2
D: 40S ribosomal protein S2
E: 40S ribosomal protein S4, X isoform
F: 40S ribosomal protein S3
G: 40S ribosomal protein S6
H: 40S ribosomal protein S7
I: 40S ribosomal protein S8
J: 40S ribosomal protein S9
K: 40S ribosomal protein S5
L: 40S ribosomal protein S11
M: 40S ribosomal protein S10
N: ribosomal protein uS15
O: ribosomal protein eS12
P: ribosomal protein uS11
Q: 40S ribosomal protein S15
R: 40S ribosomal protein S16
S: ribosomal protein eS17
T: ribosomal protein uS13
U: 40S ribosomal protein S19
V: ribosomal protein uS10
W: 40S ribosomal protein S15a
X: 40S ribosomal protein S23
Y: Isoform 3 of 40S ribosomal protein S24
Z: 40S ribosomal protein S21
a: ribosomal protein eS25
b: 40S ribosomal protein S27
c: 40S ribosomal protein S26
d: ribosomal protein eS28
e: ribosomal protein eS30
f: ribosomal protein uS14
g: 40S ribosomal protein S27a
h: ribosomal protein eL41
j: Receptor of activated protein C kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,234,81943
Polymers1,233,73838
Non-polymers1,0825
Water00
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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Protein , 4 types, 4 molecules 14Yj

#1: Protein Eukaryotic translation initiation factor 5B / eIF-5B / Translation initiation factor IF-2


Mass: 69868.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF5B, IF2, KIAA0741 / Production host: Escherichia coli (E. coli) / References: UniProt: O60841, protein-synthesizing GTPase
#4: Protein Translation initiation factor eIF1A


Mass: 10384.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#27: Protein Isoform 3 of 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 14361.046 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS24 / Production host: Homo sapiens (human) / References: UniProt: P62847
#37: 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: 34726.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RACK1, GNB2L1, HLC7, PIG21 / Production host: Homo sapiens (human) / References: UniProt: P63244

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RNA chain , 2 types, 2 molecules 23

#2: RNA chain 18S ribosomal RNA


Mass: 534544.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: RNA chain Human Met-tRNAiMet


Mass: 24231.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: GenBank: 174924

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Ribosomal protein ... , 12 types, 13 molecules BCNOPSTVadefh

#5: Protein ribosomal protein uS2


Mass: 47843.590 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#16: Protein ribosomal protein uS15


Mass: 16340.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#17: Protein ribosomal protein eS12


Mass: 13347.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#18: Protein ribosomal protein uS11


Mass: 14344.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#21: Protein ribosomal protein eS17


Mass: 15250.714 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#22: Protein ribosomal protein uS13


Mass: 16496.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#24: Protein ribosomal protein uS10


Mass: 11508.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#29: Protein ribosomal protein eS25


Mass: 8182.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#32: Protein ribosomal protein eS28


Mass: 6451.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#33: Protein ribosomal protein eS30


Mass: 5640.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#34: Protein ribosomal protein uS14


Mass: 6502.573 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#36: Protein/peptide ribosomal protein eL41


Mass: 2683.481 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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40S ribosomal protein ... , 19 types, 19 molecules DEFGHIJKLMQRUWXZbcg

#6: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 24091.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS2, RPS4 / Production host: Homo sapiens (human) / References: UniProt: P15880
#7: Protein 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29164.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS4X, CCG2, RPS4, SCAR / Production host: Homo sapiens (human) / References: UniProt: P62701
#8: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 24970.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS3, OK/SW-cl.26 / Production host: Homo sapiens (human)
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#9: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 26157.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS6, OK/SW-cl.2 / Production host: Homo sapiens (human) / References: UniProt: P62753
#10: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 21187.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS7 / Production host: Homo sapiens (human) / References: UniProt: P62081
#11: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 23945.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS8, OK/SW-cl.83 / Production host: Homo sapiens (human) / References: UniProt: P62241
#12: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 21279.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS9 / Production host: Homo sapiens (human) / References: UniProt: P46781
#13: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 21327.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS5 / Production host: Homo sapiens (human) / References: UniProt: P46782
#14: Protein 40S ribosomal protein S11 / Small ribosomal subunit protein uS17


Mass: 17170.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS11 / Production host: Homo sapiens (human) / References: UniProt: P62280
#15: Protein 40S ribosomal protein S10


Mass: 11616.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS10 / Production host: Homo sapiens (human) / References: UniProt: A0A2R8Y7H1
#19: Protein 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 13586.022 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS15, RIG / Production host: Homo sapiens (human) / References: UniProt: P62841
#20: Protein 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 15765.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS16 / Production host: Homo sapiens (human) / References: UniProt: P62249
#23: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 15409.689 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS19 / Production host: Homo sapiens (human) / References: UniProt: P39019
#25: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14734.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS15A, OK/SW-cl.82 / Production host: Homo sapiens (human) / References: UniProt: P62244
#26: Protein 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15626.392 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS23 / Production host: Homo sapiens (human) / References: UniProt: P62266
#28: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 8977.214 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS21 / Production host: Homo sapiens (human) / References: UniProt: P63220
#30: Protein 40S ribosomal protein S27 / Metallopan-stimulin 1 / MPS-1 / Small ribosomal subunit protein eS27


Mass: 9210.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27, MPS1 / Production host: Homo sapiens (human) / References: UniProt: P42677
#31: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 11341.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS26 / Production host: Homo sapiens (human) / References: UniProt: P62854
#35: Protein 40S ribosomal protein S27a / Small ribosomal subunit protein eS31


Mass: 7623.009 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPS27A, UBA80, UBCEP1 / Production host: Homo sapiens (human) / References: UniProt: P62979

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Non-polymers , 3 types, 5 molecules

#38: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#39: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#40: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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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

ComponentName: human 40S ribosomal subunit in complex with eIF1A and eIF5B
Type: CELL / Entity ID: #2-#30, #32-#33, #36-#37 / Source: MULTIPLE SOURCES
Source (natural)Organism: Homo sapiens (human)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190000 / Symmetry type: POINT
RefinementResolution: 3.2→237.11 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 23.665 / SU ML: 0.345 / ESU R: 0.539
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.28181 --
obs0.28181 579558 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: 131.797 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å21.04 Å20.57 Å2
2--0.36 Å2-0.75 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Total: 80976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.01286105
ELECTRON MICROSCOPYr_bond_other_d0.0020.01862050
ELECTRON MICROSCOPYr_angle_refined_deg1.1091.531124527
ELECTRON MICROSCOPYr_angle_other_deg1.0931.885144915
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.69955471
ELECTRON MICROSCOPYr_dihedral_angle_2_deg29.2920.1292402
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.662158758
ELECTRON MICROSCOPYr_dihedral_angle_4_deg13.29815466
ELECTRON MICROSCOPYr_chiral_restr0.0480.212703
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0269898
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0218624
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_it2.95914.40421995
ELECTRON MICROSCOPYr_mcbond_other2.95914.40321993
ELECTRON MICROSCOPYr_mcangle_it5.11721.61127429
ELECTRON MICROSCOPYr_mcangle_other5.11721.61127429
ELECTRON MICROSCOPYr_scbond_it2.66213.85564110
ELECTRON MICROSCOPYr_scbond_other2.66213.85564110
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other4.61720.75497099
ELECTRON MICROSCOPYr_long_range_B_refined7.667100934
ELECTRON MICROSCOPYr_long_range_B_other7.667100935
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.484 42867 -
obs--100 %

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