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- PDB-7qp7: Structure of the human 48S initiation complex in closed state (h4... -

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Basic information

Entry
Database: PDB / ID: 7qp7
TitleStructure of the human 48S initiation complex in closed state (h48S AUG closed)
Components
  • (40S ribosomal protein ...) x 31
  • (Eukaryotic translation initiation factor 2 subunit ...) x 2
  • (Eukaryotic translation initiation factor 3 subunit ...Eukaryotic initiation factor 3) x 11
  • 18S rRNA18S ribosomal RNA
  • 60S ribosomal protein L41
  • Eukaryotic translation initiation factor 1A, X-chromosomal
  • Initiator Met-tRNA-i
  • Receptor of activated protein C kinase 1
  • Ubiquitin-40S ribosomal protein S27a
  • mRNAMessenger RNA
KeywordsRIBOSOME / 48S / initiation / eIF3 / ternary complex / translation / open state
Function / homology
Function and homology information


positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding ...positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / Response of EIF2AK1 (HRI) to heme deficiency / translation reinitiation / negative regulation of translational initiation in response to stress / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / : / eukaryotic translation initiation factor 2 complex / IRES-dependent viral translational initiation / PERK regulates gene expression / regulation of translational initiation in response to stress / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / : / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / eukaryotic 48S preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / metal-dependent deubiquitinase activity / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / negative regulation of phagocytosis / NF-kappaB complex / rRNA modification in the nucleus and cytosol / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / pigmentation / protein kinase A binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / regulation of cell division / protein deubiquitination / Protein hydroxylation / TOR signaling / iron-sulfur cluster binding / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / 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) / Selenocysteine synthesis / monocyte chemotaxis / Formation of a pool of free 40S subunits / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / ribosomal small subunit export from nucleus / Response of EIF2AK4 (GCN2) to amino acid deficiency
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain ...Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) / Eukaryotic translation initiation factor 3 subunit H / eIF3h, C-terminal / C-terminal region of eIF3h / Eukaryotic translation initiation factor 3 subunit F / Translation initiation factor 3 complex subunit L / RNA polymerase I-associated factor PAF67 / Eukaryotic translation initiation factor 3 subunit M / eIF3 subunit M, C-terminal helix domain / eIF3 subunit M, C-terminal helix / Eukaryotic translation initiation factor 3 subunit E, C-terminal / Eukaryotic translation initiation factor 3 subunit E / Eukaryotic translation initiation factor 3 subunit E, N-terminal / eIF3 subunit 6 N terminal domain / eIF3 subunit 6 N terminal domain / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit G, N-terminal / eIF3G, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Eukaryotic translation initiation factor 3 subunit C, N-terminal domain / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit 8 N-terminus / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor eIF2A / Translation initiation factor 1A (eIF-1A), conserved site / Eukaryotic initiation factor 1A signature. / eukaryotic translation initiation factor 1A / Translation initiation factor 1A (eIF-1A) / IF2a, S1-like domain / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / Eukaryotic translation initiation factor 2 alpha subunit / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, C terminal / RNA-binding domain, S1, IF1 type / Translation initiation factor 1A / IF-1 / S1 domain IF1 type profile. / Ubiquitin-like protein FUBI / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / 40S ribosomal protein SA C-terminus / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / : / Ribosomal protein L41 / Ribosomal protein L41 / : / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e, conserved site / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S19e, conserved site / S27a-like superfamily / Ribosomal protein S26e / Ribosomal protein S26e signature. / S1 domain profile. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S17e, conserved site / Ribosomal protein S25 / : / Ribosomal protein S2, eukaryotic / Ribosomal protein S30 / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S3, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / S25 ribosomal protein / Ribosomal protein S21e signature. / Ribosomal protein S19A/S15e / Ribosomal protein S3Ae, conserved site / Ribosomal protein S30 / Ribosomal protein S12e signature. / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S19e
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 2 subunit 1 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 3 subunit F / Eukaryotic translation initiation factor 3 subunit D / Eukaryotic translation initiation factor 3 subunit H / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 2 subunit 1 / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein eS19 / Eukaryotic translation initiation factor 2 subunit 3 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein eS10 / Eukaryotic translation initiation factor 1A, X-chromosomal / Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit E / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein uS14 / Small ribosomal subunit protein uS15 / 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 eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS32 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein RACK1 / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor 3 subunit M / Eukaryotic translation initiation factor 3 subunit C / Eukaryotic translation initiation factor 3 subunit K / Eukaryotic translation initiation factor 3 subunit L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsYi, S.-H. / Petrychenko, V. / Schliep, J.E. / Goyal, A. / Linden, A. / Chari, A. / Urlaub, H. / Stark, H. / Rodnina, M.V. / Adio, S. / Fischer, N.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)Leibniz Prize (to M.V.R.) & SFB 860 Germany
Max Planck Society Germany
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Conformational rearrangements upon start codon recognition in human 48S translation initiation complex.
Authors: Sung-Hui Yi / Valentyn Petrychenko / Jan Erik Schliep / Akanksha Goyal / Andreas Linden / Ashwin Chari / Henning Urlaub / Holger Stark / Marina V Rodnina / Sarah Adio / Niels Fischer /
Abstract: Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of ...Selection of the translation start codon is a key step during protein synthesis in human cells. We obtained cryo-EM structures of human 48S initiation complexes and characterized the intermediates of codon recognition by kinetic methods using eIF1A as a reporter. Both approaches capture two distinct ribosome populations formed on an mRNA with a cognate AUG codon in the presence of eIF1, eIF1A, eIF2-GTP-Met-tRNAiMet and eIF3. The 'open' 40S subunit conformation differs from the human 48S scanning complex and represents an intermediate preceding the codon recognition step. The 'closed' form is similar to reported structures of complexes from yeast and mammals formed upon codon recognition, except for the orientation of eIF1A, which is unique in our structure. Kinetic experiments show how various initiation factors mediate the population distribution of open and closed conformations until 60S subunit docking. Our results provide insights into the timing and structure of human translation initiation intermediates and suggest the differences in the mechanisms of start codon selection between mammals and yeast.
History
DepositionJan 3, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 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 1.2Apr 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)2,165,27953
Polymers2,165,14851
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Eukaryotic translation initiation factor 3 subunit ... , 11 types, 11 molecules 134568ouvxy

#1: Protein Eukaryotic translation initiation factor 3 subunit B / Eukaryotic initiation factor 3 / eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / ...eIF3b / Eukaryotic translation initiation factor 3 subunit 9 / Prt1 homolog / hPrt1 / eIF-3-eta / eIF3 p110 / eIF3 p116


Mass: 92464.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P55884
#2: Protein Eukaryotic translation initiation factor 3 subunit K / Eukaryotic initiation factor 3 / eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / ...eIF3k / Eukaryotic translation initiation factor 3 subunit 12 / Muscle-specific gene M9 protein / PLAC-24 / eIF-3 p25 / eIF-3 p28


Mass: 25083.619 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UBQ5
#3: Protein Eukaryotic translation initiation factor 3 subunit F / Eukaryotic initiation factor 3 / eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF- ...eIF3f / Deubiquitinating enzyme eIF3f / Eukaryotic translation initiation factor 3 subunit 5 / eIF-3-epsilon / eIF3 p47


Mass: 37593.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00303, ubiquitinyl hydrolase 1
#4: Protein Eukaryotic translation initiation factor 3 subunit L / Eukaryotic initiation factor 3 / eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic ...eIF3l / Eukaryotic translation initiation factor 3 subunit 6-interacting protein / Eukaryotic translation initiation factor 3 subunit E-interacting protein


Mass: 66803.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9Y262
#5: Protein Eukaryotic translation initiation factor 3 subunit M / Eukaryotic initiation factor 3 / eIF3m / Fetal lung protein B5 / hFL-B5 / PCI domain-containing protein 1


Mass: 42555.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q7L2H7
#7: Protein Eukaryotic translation initiation factor 3 subunit H / Eukaryotic initiation factor 3 / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


Mass: 39979.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15372
#43: Protein Eukaryotic translation initiation factor 3 subunit G / Eukaryotic initiation factor 3 / eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit ...eIF3g / Eukaryotic translation initiation factor 3 RNA-binding subunit / eIF-3 RNA-binding subunit / Eukaryotic translation initiation factor 3 subunit 4 / eIF-3-delta / eIF3 p42 / eIF3 p44


Mass: 35662.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O75821
#47: Protein Eukaryotic translation initiation factor 3 subunit A / Eukaryotic initiation factor 3 / eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 ...eIF3a / Eukaryotic translation initiation factor 3 subunit 10 / eIF-3-theta / eIF3 p167 / eIF3 p180 / eIF3 p185


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


Mass: 52281.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P60228
#50: Protein Eukaryotic translation initiation factor 3 subunit D / Eukaryotic initiation factor 3 / eIF3d / Eukaryotic translation initiation factor 3 subunit 7 / eIF-3-zeta / eIF3 p66


Mass: 64060.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15371
#51: Protein Eukaryotic translation initiation factor 3 subunit C / Eukaryotic initiation factor 3 / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 105503.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q99613

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RNA chain , 3 types, 3 molecules 7Aw

#6: RNA chain mRNA / Messenger RNA


Mass: 82412.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#9: RNA chain 18S rRNA / 18S ribosomal RNA


Mass: 603102.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#49: RNA chain Initiator Met-tRNA-i


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

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

#10: 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
#11: 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
#12: 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
#13: 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
#14: 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
#15: 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
#16: 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
#17: 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
#18: 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
#19: 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
#20: 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
#21: 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
#22: 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
#23: 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
#24: 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
#25: 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
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: 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
#32: 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
#33: 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
#35: 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
#36: 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
#37: 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
#38: 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
#39: 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
#41: 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
#42: 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

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Protein , 3 types, 3 molecules ckq

#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
#40: 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
#44: Protein Eukaryotic translation initiation factor 1A, X-chromosomal / eIF-1A X isoform / Eukaryotic translation initiation factor 4C / eIF-4C


Mass: 16488.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF1AX, EIF1A, EIF4C / Production host: Escherichia coli (E. coli) / References: UniProt: P47813

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Eukaryotic translation initiation factor 2 subunit ... , 2 types, 2 molecules rt

#45: Protein Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 36161.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P05198
#46: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 51178.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P41091, protein-synthesizing GTPase

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Protein/peptide / Non-polymers , 2 types, 3 molecules 9

#52: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Protein/peptide 60S ribosomal protein L41 / / HG12 / Large ribosomal subunit protein eL41


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

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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: Human 48S initiation complex 40S-eIF1-eIF1A-eIF2-eIF3-tRNA-Met-mRNA
Type: RIBOSOME / Entity ID: #1-#51 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.5
Details: 20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R3.5/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Details: Aberration corrections performed using Cs image corrector (CEOS company)
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 0.01 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15544
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: UCSF ChimeraX / Version: 1.3/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: Windows / Type: package
EM software
IDNameVersionCategory
7Coot0.9.4model fitting
8UCSF ChimeraX1.2model fitting
10RELION3.1initial Euler assignment
11RELIONfinal Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14ISOLDE1.1model refinement
15Coot0.9.4model refinement
16UCSF ChimeraX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 990486
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 364950 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: RSCC
Atomic model buildingPDB-ID: 6ZMW

6zmw


Accession code: 6ZMW / Source name: PDB / Type: experimental model

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