[English] 日本語
Yorodumi
- PDB-6fec: Human cap-dependent 48S pre-initiation complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6fec
TitleHuman cap-dependent 48S pre-initiation complex
Components
  • (40S ribosomal protein ...) x 31
  • (EUKARYOTIC TRANSLATION INITIATION FACTOR ...) x 14
  • 18S ribosomal RNA
  • Messenger RNA (26-MER)
  • Receptor of activated protein C kinase 1
  • Transfer RNA (75-MER)
  • Ubiquitin-40S ribosomal protein S27a
KeywordsRIBOSOME / Translation initiation / 48S complex / capped mRNA / initiation factor 4B / start codon recognition
Function / homology
Function and homology information


eukaryotic translation initiation factor 4F complex assembly / RNA strand-exchange activity / positive regulation of mRNA binding / viral translational termination-reinitiation / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S ...eukaryotic translation initiation factor 4F complex assembly / RNA strand-exchange activity / positive regulation of mRNA binding / viral translational termination-reinitiation / Cellular response to mitochondrial stress / eukaryotic translation initiation factor 3 complex, eIF3e / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / methionyl-initiator methionine tRNA binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / eukaryotic translation initiation factor 3 complex, eIF3m / PERK regulates gene expression / RNA strand annealing activity / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / eukaryotic translation initiation factor 4F complex / formation of cytoplasmic translation initiation complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / Deadenylation of mRNA / eukaryotic 48S preinitiation complex / M-decay: degradation of maternal mRNAs by maternally stored factors / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / negative regulation of peptidyl-serine phosphorylation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / TNFR1-mediated ceramide production / protein-synthesizing GTPase / negative regulation of DNA repair / negative regulation of RNA splicing / mammalian oogenesis stage / regulation of translational initiation / supercoiled DNA binding / activation-induced cell death of T cells / neural crest cell differentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / NF-kappaB complex / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / translation at presynapse / Formation of the ternary complex, and subsequently, the 43S complex / negative regulation of phagocytosis / erythrocyte homeostasis / rRNA modification in the nucleus and cytosol / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / pigmentation / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / negative regulation of Wnt signaling pathway / negative regulation of translational frameshifting / Protein hydroxylation / BH3 domain binding / TOR signaling / SARS-CoV-1 modulates host translation machinery / regulation of cell division / mTORC1-mediated signalling / T cell proliferation involved in immune response / Peptide chain elongation / iron-sulfur cluster binding / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ribosomal small subunit binding / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / phagocytic cup / 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 / erythrocyte development / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
Similarity search - Function
Eukaryotic translation initiation factor 4B / 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 6 N terminal 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 ...Eukaryotic translation initiation factor 4B / 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 6 N terminal 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 / Eukaryotic translation initiation factor 3 subunit K / Translation initiation factor 3, subunit 12, N-terminal, eukaryotic / Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7 / Initiation factor eIF2 gamma, C-terminal / Initiation factor eIF2 gamma, domain 2 / Initiation factor eIF2 gamma, GTP-binding domain / Initiation factor eIF2 gamma, C terminal / : / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / 40S ribosomal protein SA / 40S ribosomal protein SA, C-terminal domain / 40S ribosomal protein SA C-terminus / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ubiquitin-like protein FUBI / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S2, eukaryotic / S27a-like superfamily / Translation elongation factor EFTu-like, domain 2 / 40S Ribosomal protein S10 / : / Ribosomal protein S7e signature. / Plectin/S10, N-terminal / Plectin/S10 domain / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S27a / Ribosomal protein S17e, conserved site / Ribosomal protein S27a / Ribosomal protein S17e signature. / Ribosomal protein S27a / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S2, eukaryotic/archaeal / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S27e signature. / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / Ribosomal protein S4e, N-terminal, conserved site / Ribosomal protein S4e signature. / Ribosomal protein S3, eukaryotic/archaeal / Elongation factor Tu domain 2 / Ribosomal protein S8e, conserved site / Ribosomal protein S8e signature. / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein S19A/S15e / Ribosomal protein S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / 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 S23, eukaryotic/archaeal / Ribosomal protein S6/S6e/A/B/2, conserved site / Ribosomal protein S6e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S27 / Ribosomal protein S27, zinc-binding domain superfamily / Ribosomal protein S27 / Ribosomal protein S17, archaeal/eukaryotic / Ribosomal protein S8e / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal S3Ae family / Ribosomal protein S28e conserved site
Similarity search - Domain/homology
: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Eukaryotic translation initiation factor 4B / Small ribosomal subunit protein eS12 ...: / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein eS17 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein uS3 / Eukaryotic translation initiation factor 4B / Small ribosomal subunit protein eS12 / 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 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 eS28 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein RACK1 / Eukaryotic translation initiation factor 3 subunit M / 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: 6.3 Å
AuthorsSchaffitzel, C. / Schaffitzel, C.
Funding support Belgium, 2items
OrganizationGrant numberCountry
European Research Council281331 Belgium
EMBL-RFBR15-54-74001 Belgium
CitationJournal: Nucleic Acids Res / Year: 2018
Title: Structure of a human cap-dependent 48S translation pre-initiation complex.
Authors: Boris Eliseev / Lahari Yeramala / Alexander Leitner / Manikandan Karuppasamy / Etienne Raimondeau / Karine Huard / Elena Alkalaeva / Ruedi Aebersold / Christiane Schaffitzel /
Abstract: Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load ...Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition.
History
DepositionDec 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 3, 2018Group: Data collection / Refinement description / Category: computing / refine
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4242
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: Eukaryotic translation initiation factor 3 subunit A
2: Eukaryotic translation initiation factor 3 subunit C
3: Eukaryotic translation initiation factor 3 subunit E
4: Eukaryotic translation initiation factor 3 subunit F
5: Eukaryotic translation initiation factor 3 subunit H
6: Eukaryotic translation initiation factor 3 subunit K
7: Eukaryotic translation initiation factor 3 subunit L
8: Eukaryotic translation initiation factor 3 subunit M
9: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D
A: 18S ribosomal RNA
F: Messenger RNA (26-MER)
G: 40S ribosomal protein S11
H: 40S ribosomal protein S16
I: 40S ribosomal protein S4, X isoform
J: 40S ribosomal protein S29
K: 40S ribosomal protein S9
L: 40S ribosomal protein S18
N: Transfer RNA (75-MER)
P: Eukaryotic translation initiation factor 2 subunit 1
Q: 40S ribosomal protein S23
R: 40S ribosomal protein S19
S: Eukaryotic translation initiation factor 2 subunit 3
U: 40S ribosomal protein S5
V: 40S ribosomal protein S30
W: 40S ribosomal protein S25
X: 40S ribosomal protein S7
Y: 40S ribosomal protein S27
Z: 40S ribosomal protein S13
a: 40S ribosomal protein S15a
b: 40S ribosomal protein S21
c: 40S ribosomal protein S2
d: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)
e: 40S ribosomal protein S17
f: 40S ribosomal protein SA
g: 40S ribosomal protein S3
h: 40S ribosomal protein S20
i: 40S ribosomal protein S3a
j: 40S ribosomal protein S14
k: 40S ribosomal protein S26
l: 40S ribosomal protein S28
m: Receptor of activated protein C kinase 1
n: 40S ribosomal protein S15
o: 40S ribosomal protein S8
p: Ubiquitin-40S ribosomal protein S27a
q: 40S ribosomal protein S6
r: 40S ribosomal protein S12
s: 40S ribosomal protein S24
t: 40S ribosomal protein S10
u: Eukaryotic translation initiation factor 4B
w: Eukaryotic translation initiation factor 3 subunit B


Theoretical massNumber of molelcules
Total (without water)2,006,44050
Polymers2,006,44050
Non-polymers00
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking, h-48S pre-IC formation was confirmed by toe-printing and by cross-linking mass spectrometry.
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
EUKARYOTIC TRANSLATION INITIATION FACTOR ... , 14 types, 14 molecules 123456789PSduw

#1: Protein Eukaryotic translation initiation factor 3 subunit A / 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: 164902.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#2: Protein Eukaryotic translation initiation factor 3 subunit C / eIF3c / Eukaryotic translation initiation factor 3 subunit 8 / eIF3 p110


Mass: 97923.547 Da / Num. of mol.: 1 / Mutation: A577Y / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#3: Protein Eukaryotic translation initiation factor 3 subunit E / 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) / Cell line: hela / References: UniProt: P60228
#4: Protein Eukaryotic translation initiation factor 3 subunit F / 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: 37846.730 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Hela / References: ubiquitinyl hydrolase 1
#5: Protein Eukaryotic translation initiation factor 3 subunit H / eIF3h / Eukaryotic translation initiation factor 3 subunit 3 / eIF-3-gamma / eIF3 p40 subunit


Mass: 39952.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#6: Protein Eukaryotic translation initiation factor 3 subunit K / 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: 25129.709 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: Q9UBQ5
#7: Protein Eukaryotic translation initiation factor 3 subunit L / 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: 66804.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: Q9Y262
#8: Protein Eukaryotic translation initiation factor 3 subunit M / 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) / Cell line: hela / References: UniProt: Q7L2H7
#9: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D


Mass: 42203.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#19: Protein Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit alpha / eIF-2alpha


Mass: 30633.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#22: Protein Eukaryotic translation initiation factor 2 subunit 3 / Eukaryotic translation initiation factor 2 subunit gamma X / eIF-2gX


Mass: 45862.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P41091
#32: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)


Mass: 2103.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)
#49: Protein Eukaryotic translation initiation factor 4B / eIF-4B


Mass: 72324.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4B / Plasmid: pFastBac_eIF4B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P23588
#50: Protein Eukaryotic translation initiation factor 3 subunit B / 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: 124402.336 Da / Num. of mol.: 1 / Mutation: D104E, Y124F / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela

-
RNA chain , 3 types, 3 molecules AFN

#10: RNA chain 18S ribosomal RNA


Mass: 572789.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#11: RNA chain Messenger RNA (26-MER)


Mass: 8238.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: beta globin derived / Plasmid: pET28a-MVHL-STOP2 / Production host: Escherichia coli (E. coli)
#18: RNA chain Transfer RNA (75-MER)


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

+
40S ribosomal protein ... , 31 types, 31 molecules GHIJKLQRUVWXYZabcefghijklnoqrst

#12: 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: hela / References: UniProt: P62280
#13: Protein 40S ribosomal protein S16 / Small ribosomal subunit protein uS9


Mass: 15975.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62249
#14: Protein 40S ribosomal protein S4, X isoform / SCR10 / Single copy abundant mRNA protein / Small ribosomal subunit protein eS4


Mass: 29658.920 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62701
#15: Protein 40S ribosomal protein S29 / Small ribosomal subunit protein uS14


Mass: 6364.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62273
#16: Protein 40S ribosomal protein S9 / Small ribosomal subunit protein uS4


Mass: 21266.166 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P46781
#17: Protein 40S ribosomal protein S18 / Ke-3 / Ke3 / Small ribosomal subunit protein uS13


Mass: 16170.774 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62269
#20: Protein 40S ribosomal protein S23 / Small ribosomal subunit protein uS12


Mass: 15757.587 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62266
#21: Protein 40S ribosomal protein S19 / Small ribosomal subunit protein eS19


Mass: 15812.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#23: Protein 40S ribosomal protein S5 / Small ribosomal subunit protein uS7


Mass: 21525.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P46782
#24: Protein 40S ribosomal protein S30 / Small ribosomal subunit protein eS30


Mass: 6741.048 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62861
#25: Protein 40S ribosomal protein S25 / Small ribosomal subunit protein eS25


Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62851
#26: Protein 40S ribosomal protein S7 / Small ribosomal subunit protein eS7


Mass: 21716.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62081
#27: 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: hela / References: UniProt: P42677
#28: Protein 40S ribosomal protein S13 / Small ribosomal subunit protein uS15


Mass: 17128.191 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62277
#29: Protein 40S ribosomal protein S15a / Small ribosomal subunit protein uS8


Mass: 14734.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62244
#30: Protein 40S ribosomal protein S21 / Small ribosomal subunit protein eS21


Mass: 8896.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#31: Protein 40S ribosomal protein S2 / 40S ribosomal protein S4 / Protein LLRep3 / Small ribosomal subunit protein uS5


Mass: 24814.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#33: Protein 40S ribosomal protein S17 / Small ribosomal subunit protein eS17


Mass: 14578.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P08708
#34: 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: 23360.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08865
#35: Protein 40S ribosomal protein S3 / Small ribosomal subunit protein uS3


Mass: 25158.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
References: UniProt: P23396, DNA-(apurinic or apyrimidinic site) lyase
#36: Protein 40S ribosomal protein S20 / Small ribosomal subunit protein uS10


Mass: 11765.890 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P60866
#37: Protein 40S ribosomal protein S3a / Small ribosomal subunit protein eS1 / v-fos transformation effector protein / Fte-1


Mass: 24944.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P61247
#38: Protein 40S ribosomal protein S14 / Small ribosomal subunit protein uS11


Mass: 14544.659 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62263
#39: Protein 40S ribosomal protein S26 / Small ribosomal subunit protein eS26


Mass: 11315.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela
#40: Protein 40S ribosomal protein S28 / Small ribosomal subunit protein eS28


Mass: 7263.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62857
#42: Protein 40S ribosomal protein S15 / RIG protein / Small ribosomal subunit protein uS19


Mass: 15151.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62841
#43: Protein 40S ribosomal protein S8 / Small ribosomal subunit protein eS8


Mass: 23902.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62241
#45: Protein 40S ribosomal protein S6 / Phosphoprotein NP33 / Small ribosomal subunit protein eS6


Mass: 27471.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62753
#46: Protein 40S ribosomal protein S12 / Small ribosomal subunit protein eS12


Mass: 13766.122 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P25398
#47: Protein 40S ribosomal protein S24 / Small ribosomal subunit protein eS24


Mass: 15188.970 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62847
#48: Protein 40S ribosomal protein S10 / Small ribosomal subunit protein eS10


Mass: 11773.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P46783

-
Protein , 2 types, 2 molecules mp

#41: 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: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P63244
#44: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8358.903 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: hela / References: UniProt: P62979

-
Non-polymers , 1 types, 415 molecules

#51: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1human cap-dependent 48S translation pre-initiation complexRIBOSOME#1-#500MULTIPLE SOURCES
2human cap-dependent 48S translation pre-initiation complexRIBOSOME#1-#10, #12-#48, #501NATURAL
3mRNACOMPLEX#111RECOMBINANT
4Eukaryotic translation initiation factor 4BCOMPLEX#491RECOMBINANT
Molecular weightValue: 2.0 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Escherichia coli (E. coli)562
24Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
Details: 20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
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 FIELD / Nominal magnification: 112000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2.1particle selectione2boxer.py
4CTFFIND4CTF correction
7UCSF Chimera1.1model fitting
9REFMAC5.8.0194model refinement
10RELION1.4initial Euler assignment
11RELION1.4final Euler assignment
12RELION1.4classification
13RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50604 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
RefinementResolution: 6.3→270 Å / Cor.coef. Fo:Fc: 0.961 / SU B: 135.967 / SU ML: 0.877
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.37479 --
obs0.37479 95026 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: 105.458 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å2-0.57 Å2-1.05 Å2
2--4.34 Å2-2.56 Å2
3----4.98 Å2
Refinement stepCycle: 1 / Total: 32425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0180.01932657
ELECTRON MICROSCOPYr_bond_other_d0.0060.0229932
ELECTRON MICROSCOPYr_angle_refined_deg1.9151.95444216
ELECTRON MICROSCOPYr_angle_other_deg1.376369307
ELECTRON MICROSCOPYr_dihedral_angle_1_deg9.59253945
ELECTRON MICROSCOPYr_dihedral_angle_2_deg41.46324.4321638
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.998155854
ELECTRON MICROSCOPYr_dihedral_angle_4_deg15.94215222
ELECTRON MICROSCOPYr_chiral_restr0.150.24935
ELECTRON MICROSCOPYr_gen_planes_refined0.0090.0236132
ELECTRON MICROSCOPYr_gen_planes_other0.0050.026629
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_it18.67439.39615825
ELECTRON MICROSCOPYr_mcbond_other18.67339.39715824
ELECTRON MICROSCOPYr_mcangle_it32.73159.03619763
ELECTRON MICROSCOPYr_mcangle_other32.73159.03619764
ELECTRON MICROSCOPYr_scbond_it19.88336.15616832
ELECTRON MICROSCOPYr_scbond_other19.88336.15616833
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other37.15455.10124454
ELECTRON MICROSCOPYr_long_range_B_refined63.43958918
ELECTRON MICROSCOPYr_long_range_B_other63.43958919
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 6.3→6.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.519 7099 -
obs--100 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more