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- PDB-5k0y: m48S late-stage initiation complex, purified from rabbit reticulo... -

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Basic information

Entry
Database: PDB / ID: 5k0y
Titlem48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face
Components
  • (40S ribosomal protein ...) x 7
  • (Eukaryotic translation initiation factor 3 subunit ...) x 3
  • (eukaryotic initiation factor 2 ...) x 2
  • (ribosomal protein ...) x 26
  • 18S ribosomal RNA
  • Eukaryotic translation initiation factor 2 subunit 1
  • mRNA
  • tRNA
KeywordsTRANSLATION / eukaryotic translation initiation / ribosome / eIF3 peripheral subunits / cryo-EM
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / cellular response to chemical stress / protein-synthesizing GTPase ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3m / eukaryotic translation initiation factor 2 complex / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / eukaryotic 43S preinitiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / cellular response to chemical stress / protein-synthesizing GTPase / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / 90S preribosome / L13a-mediated translational silencing of Ceruloplasmin expression / phagocytic cup / regulation of translational fidelity / laminin binding / ribosomal small subunit export from nucleus / rough endoplasmic reticulum / translation regulator activity / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor activity / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to endoplasmic reticulum stress / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / spindle / cytoplasmic stress granule / rRNA processing / rhythmic process / positive regulation of canonical Wnt signaling pathway / regulation of translation / ribosome binding / virus receptor activity / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytosolic large ribosomal subunit / cytoplasmic translation / cell differentiation / tRNA binding / mitochondrial inner membrane / postsynaptic density / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / DNA repair / GTPase activity / mRNA binding / apoptotic process / synapse / dendrite / centrosome / GTP binding / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / DNA binding / RNA binding / zinc ion binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Translation initiation factor 2, beta subunit / EIF3I / 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 I / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding ...Translation initiation factor 2, beta subunit / EIF3I / 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 I / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Translation initiation factor IF2/IF5 / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / 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 / Translation initiation factor 2, alpha subunit / Translation initiation factor 2, alpha subunit, middle domain superfamily / Translation initiation factor 2, alpha subunit, C-terminal / IF2a, S1-like domain / Eukaryotic translation initiation factor 2 alpha subunit / : / 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 / S1 domain profile. / : / Ribosomal protein S26e signature. / Ribosomal protein S21e, conserved site / Ribosomal protein S21e signature. / Ribosomal protein S26e / Ribosomal protein S26e superfamily / Ribosomal protein S26e / : / Ribosomal protein S12e signature. / Ribosomal protein S12e / Small (40S) ribosomal subunit Asc1/RACK1 / Ribosomal protein S21e / Ribosomal protein S21e superfamily / Ribosomal protein S21e / Ribosomal protein S19e, conserved site / Ribosomal protein S19e signature. / Ribosomal protein S2, eukaryotic / S27a-like superfamily / 40S Ribosomal protein S10 / Translation elongation factor EFTu-like, domain 2 / Plectin/S10, N-terminal / Plectin/S10 domain / : / Ribosomal protein S7e signature. / Ribosomal protein S10, eukaryotic/archaeal / Ribosomal protein S30 / Ribosomal protein S30 / Ribosomal protein S17e, conserved site / Ribosomal protein S17e signature. / Ribosomal protein S25 / S25 ribosomal protein / Ribosomal protein S8e subdomain, eukaryotes / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S2, eukaryotic/archaeal / Ribosomal protein S3Ae, conserved site / Ribosomal protein S3Ae signature. / 40S ribosomal protein S29/30S ribosomal protein S14 type Z / Ribosomal protein S3, eukaryotic/archaeal / Elongation factor Tu domain 2 / 40S ribosomal protein S4, C-terminal domain / 40S ribosomal protein S4 C-terminus / 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 S17e / Ribosomal protein S17e-like superfamily / Ribosomal S17 / Ribosomal protein S6, eukaryotic / Ribosomal protein S7e / Ribosomal protein S7e / Ribosomal protein L7, eukaryotic / 40S ribosomal protein S1/3, eukaryotes / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 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
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 ...: / : / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein eS12 / Small ribosomal subunit protein uS9 / Small ribosomal subunit protein uS10 / Small ribosomal subunit protein RACK1 / Ubiquitin-ribosomal protein eS31 fusion protein / Small ribosomal subunit protein uS15 / protein-synthesizing GTPase / Small ribosomal subunit protein eS7 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS11 / Eukaryotic translation initiation factor 2 subunit 1 / Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein / Small ribosomal subunit protein eS25 / Small ribosomal subunit protein eS26 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein eS28 / Small ribosomal subunit protein eS8 / Small ribosomal subunit protein eS4 / Small ribosomal subunit protein eS6 / Small ribosomal subunit protein eS21 / Small ribosomal subunit protein eS19 / Small ribosomal subunit protein eS1 / Small ribosomal subunit protein uS3 / Small ribosomal subunit protein uS13 / Small ribosomal subunit protein eS10 / Small ribosomal subunit protein uS17 / 40S ribosomal protein S24 / Small ribosomal subunit protein eS17 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS2 / Small ribosomal subunit protein eS27 / Small ribosomal subunit protein uS19 / Small ribosomal subunit protein uS14 / Eukaryotic translation initiation factor 3 subunit G / Eukaryotic translation initiation factor 3 subunit I / Translation initiation factor 2 subunit beta / Small ribosomal subunit protein uS7
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsSimonetti, A. / Brito Querido, J. / Myasnikov, A.G. / Mancera-Martinez, E. / Renaud, A. / Kuhn, L. / Hashem, Y.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyatRAction program ANR CryoEM80S France
French National Research AgencyANR-10-LABX-0036_NETRNA France
CitationJournal: Mol Cell / Year: 2016
Title: eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition.
Authors: Angelita Simonetti / Jailson Brito Querido / Alexander G Myasnikov / Eder Mancera-Martinez / Adeline Renaud / Lauriane Kuhn / Yaser Hashem /
Abstract: mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal ...mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.0Jul 13, 2016Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Revision 1.0Jul 13, 2016Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
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Revision 1.1Aug 3, 2016Group: Database references
Revision 1.2Aug 2, 2017Group: Data collection / Derived calculations / Category: em_software / struct_conn / Item: _em_software.name
Revision 1.3Apr 18, 2018Group: Data collection / Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 1.4May 7, 2025Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _em_admin.last_update / _struct_ref.db_name
Revision 1.1May 7, 2025Data content type: EM metadata
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
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Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
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Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _em_admin.last_update / _struct_ref.db_name

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Structure visualization

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Assembly

Deposited unit
N: tRNA
A: 18S ribosomal RNA
F: mRNA
P: Eukaryotic translation initiation factor 2 subunit 1
G: ribosomal protein uS17
H: ribosomal protein uS9
I: 40S ribosomal protein S4
J: ribosomal protein uS14
K: Ribosomal protein S9 (Predicted)
L: ribosomal protein uS13
M: Eukaryotic translation initiation factor 3 subunit G
O: Eukaryotic translation initiation factor 3 subunit G
Q: ribosomal protein uS12
R: ribosomal protein eS19
S: eukaryotic initiation factor 2 Gamma subunit (eIF2-Gamma)
T: Eukaryotic translation initiation factor 3 subunit I
U: ribosomal protein uS7
V: ribosomal protein eS30
W: ribosomal protein eS25
X: ribosomal protein eS7
Y: 40S ribosomal protein S27
Z: ribosomal protein uS15
a: ribosomal protein uS8
b: 40S ribosomal protein S21
c: ribosomal protein uS5
d: eukaryotic initiation factor 2 subunit Beta (eIF2-Beta)
e: ribosomal protein eS17
f: ribosomal protein uS2
g: ribosomal protein uS3
h: ribosomal protein uS10
i: ribosomal protein eS1
j: ribosomal protein uS11
k: ribosomal protein eS26
l: ribosomal protein eS28
m: ribosomal protein RACK1
n: ribosomal protein uS19
o: 40S ribosomal protein S8
p: ribosomal protein eS31
q: 40S ribosomal protein S6
r: 40S ribosomal protein S12
s: 40S ribosomal protein S24
t: ribosomal protein eS10


Theoretical massNumber of molelcules
Total (without water)1,291,31742
Polymers1,291,31742
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area238270 Å2
ΔGint-1682 kcal/mol
Surface area422210 Å2
MethodPISA

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Components

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RNA chain , 3 types, 3 molecules NAF

#1: RNA chain tRNA


Mass: 24231.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: tRNAiMet / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: GENBANK: 655840029
#2: RNA chain 18S ribosomal RNA


Mass: 572789.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: GENBANK: 283837872
#3: RNA chain mRNA


Mass: 9603.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Beta-Globin mRNA / Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit)

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Protein , 1 types, 1 molecules P

#4: Protein Eukaryotic translation initiation factor 2 subunit 1


Mass: 30633.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: EIF2S1 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1T2G4

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Ribosomal protein ... , 26 types, 26 molecules GHJKLQRUVWXZacefghijklmnpt

#5: Protein ribosomal protein uS17


Mass: 18468.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LOC100347468 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TRM4
#6: Protein ribosomal protein uS9


Mass: 15975.753 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS16 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SGX4
#8: Protein ribosomal protein uS14


Mass: 6364.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LOC100337712 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1U7M4
#9: Protein Ribosomal protein S9 (Predicted)


Mass: 21266.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS9 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: B7NZS8
#10: Protein ribosomal protein uS13


Mass: 16170.774 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS18 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPG3
#13: Protein ribosomal protein uS12


Mass: 15757.587 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SZ47*PLUS
#14: Protein ribosomal protein eS19


Mass: 15812.286 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LOC100345774 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN62
#17: Protein ribosomal protein uS7


Mass: 21525.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS5 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFM5, UniProt: U3KMN4*PLUS
#18: Protein ribosomal protein eS30


Mass: 6741.048 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: FAU / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1T8A2
#19: Protein ribosomal protein eS25


Mass: 8526.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS25 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TDB3
#20: Protein ribosomal protein eS7


Mass: 21716.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS7 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SVB0
#22: Protein ribosomal protein uS15


Mass: 17128.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS13 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SP51
#23: Protein ribosomal protein uS8


Mass: 14734.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS15A / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TG89
#25: Protein ribosomal protein uS5


Mass: 24814.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TUT9*PLUS
#27: Protein ribosomal protein eS17


Mass: 14578.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS17 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TU13
#28: Protein ribosomal protein uS2


Mass: 23360.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TWL4*PLUS
#29: Protein ribosomal protein uS3


Mass: 25158.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TNM3*PLUS
#30: Protein ribosomal protein uS10


Mass: 11765.890 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SIZ2*PLUS
#31: Protein ribosomal protein eS1


Mass: 24944.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS3A / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TN72
#32: Protein ribosomal protein uS11


Mass: 14544.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1T1F0*PLUS
#33: Protein ribosomal protein eS26


Mass: 11315.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS26 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TFE8
#34: Protein ribosomal protein eS28


Mass: 7263.394 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS28 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TIB4
#35: Protein ribosomal protein RACK1


Mass: 34669.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: GNB2L1 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4
#36: Protein ribosomal protein uS19


Mass: 15151.948 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LOC103349305 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1U0Q2
#38: Protein ribosomal protein eS31


Mass: 8358.903 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LOC100348379 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SK22
#42: Protein ribosomal protein eS10


Mass: 11773.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS10 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TPV3, UniProt: G1T168*PLUS

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40S ribosomal protein ... , 7 types, 7 molecules IYboqrs

#7: Protein 40S ribosomal protein S4


Mass: 29658.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS4X / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TK17
#21: Protein 40S ribosomal protein S27


Mass: 9480.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS27 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TZ76
#24: Protein 40S ribosomal protein S21


Mass: 8896.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS21 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM82
#37: Protein 40S ribosomal protein S8


Mass: 23902.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS8 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TJW1
#39: Protein 40S ribosomal protein S6


Mass: 27471.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: LOC100339133, RPS6 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TM55
#40: Protein 40S ribosomal protein S12


Mass: 13766.122 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS12 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SFR8
#41: Protein 40S ribosomal protein S24


Mass: 15188.970 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: RPS24 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1TS40

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Eukaryotic translation initiation factor 3 subunit ... , 3 types, 3 molecules MOT

#11: Protein/peptide Eukaryotic translation initiation factor 3 subunit G / 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: 4124.495 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3G, EIF3S4 / Production host: Homo sapiens (human) / References: UniProt: O75821
#12: Protein Eukaryotic translation initiation factor 3 subunit G / 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: 8675.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF3G, EIF3S4 / Production host: Homo sapiens (human) / References: UniProt: O75821
#16: Protein Eukaryotic translation initiation factor 3 subunit I / eIF3i / Eukaryotic translation initiation factor 3 subunit 2 / eIF-3-beta / eIF3 p36


Mass: 37039.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: EIF3I, EIF3S2 / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: Q5IH81

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Eukaryotic initiation factor 2 ... , 2 types, 2 molecules Sd

#15: Protein eukaryotic initiation factor 2 Gamma subunit (eIF2-Gamma)


Mass: 45862.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: G1SRA8*PLUS
#26: Protein/peptide eukaryotic initiation factor 2 subunit Beta (eIF2-Beta)


Mass: 2103.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Oryctolagus cuniculus (rabbit) / References: UniProt: Q97W59*PLUS

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Details

Has protein modificationY

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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: m48S late-stage initiation complex, purified from rabbit reticulocytes lysates, displaying eIF2 ternary complex and eIF3 i and g subunits relocated to the intersubunit face
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 2 MDa / Experimental value: NO
Buffer solutionpH: 7.6
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 800 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 24 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5700
Image scansSampling size: 14 µm / Movie frames/image: 7 / Used frames/image: 2-8

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Processing

EM software
IDNameVersionCategory
1Xmipp1.3particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7VMDmodel fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
13VMDmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 475000 / Algorithm: FOURIER SPACE / Num. of class averages: 10 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 4KZY

4kzy


Accession code: 4KZY / Source name: PDB / Type: experimental model

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