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

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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 ...Eukaryotic initiation factor 3) x 3
  • (eukaryotic initiation factor 2 ...) x 2
  • (ribosomal protein ...) x 26
  • 18S ribosomal RNA
  • Eukaryotic translation initiation factor 2 subunit 1
  • mRNAMessenger RNA
  • tRNATransfer RNA
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 / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / ribosomal subunit / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / ribosomal subunit / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / regulation of translational fidelity / translational initiation / translation initiation factor activity / DNA-(apurinic or apyrimidinic site) lyase / small-subunit processome / ribosomal small subunit biogenesis / cytoplasmic stress granule / cytosolic small ribosomal subunit / tRNA binding / cell differentiation / structural constituent of ribosome / translation / mRNA binding / GTPase activity / synapse / GTP binding / nucleolus / perinuclear region of cytoplasm / RNA binding / cytosol / cytoplasm
Similarity search - Function
Translation initiation factor 2, beta subunit / 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 / 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 / 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 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / 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 / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Ribosomal protein S26e signature. / S1 domain profile. / Ribosomal protein S21e signature. / Ribosomal protein S30 / Ribosomal protein S3Ae, conserved site / Ribosomal protein S12e signature. / Ribosomal protein S27a / 40S ribosomal protein S1/3, eukaryotes / Ribosomal S17 / Ribosomal protein S19e signature. / Ribosomal protein S19e / 40S Ribosomal protein S10 / 40S ribosomal protein S4 C-terminus / Ribosomal_S17 N-terminal / Plectin/S10, N-terminal / Ribosomal protein S3Ae / Ribosomal S3Ae family / Ribosomal protein S7e / Plectin/S10 domain / Ribosomal protein S5/S7, eukaryotic/archaeal / RS4NT (NUC023) domain / Ribosomal protein S27 / Ribosomal S3Ae family / Ribosomal protein S17e signature. / Ribosomal protein S28e / Ribosomal family S4e / Ribosomal protein S7e signature. / Ribosomal protein S6e / Ribosomal protein S3Ae signature. / Ribosomal protein S27e signature. / Ribosomal protein S4e signature. / Ribosomal protein S8e signature. / Translation elongation factor EFTu-like, domain 2 / Ribosomal S24e conserved site / Ribosomal protein S24e signature. / Ribosomal protein S24e / Ribosomal protein S24e / Ribosomal protein S6e signature. / Ribosomal protein S28e signature. / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Ribosomal protein S8e / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Ribosomal protein S2 signature 2. / Ubiquitin domain signature. / KH domain / Ribosomal protein L30 signature. / Ribosomal protein S3, C-terminal domain / Ribosomal protein S3 signature. / Ribosomal protein S10 signature. / Ribosomal protein S14 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S19 / Ribosomal protein S2 signature 1. / Ribosomal protein S2 / Type-2 KH domain profile. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S13/S18 / Ribosomal protein S19 signature. / Ribosomal protein S14p/S29e / Ribosomal protein S7 signature. / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein S13 signature. / Ribosomal protein S5/S7 / Ribosomal protein S7 domain
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 / Plectin/eS10 N-terminal domain-containing protein / 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 / Ribosomal protein S5
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 1.1Aug 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

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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
Water0
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 / Transfer RNA


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: REF: 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: REF: 283837872
#3: RNA chain mRNA / Messenger RNA


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) / Ribosome


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 / 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: 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 / 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: 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 / Eukaryotic initiation factor 3 / 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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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 FIELDBright-field microscopy / 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

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