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- EMDB-10774: Structure of a human 48S translational initiation complex - eIF2-TC -

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Basic information

Entry
Database: EMDB / ID: EMD-10774
TitleStructure of a human 48S translational initiation complex - eIF2-TC
Map data
Sample
  • Complex: 48S initiation complex
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 2
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • RNA: Initiator methionine tRNA
    • RNA: mRNA
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3
Keywordsribosome / translation / initiation complex
Function / homology
Function and homology information


male germ cell proliferation / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency ...male germ cell proliferation / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / response to kainic acid / Cellular response to mitochondrial stress / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / Recycling of eIF2:GDP / negative regulation of translational initiation in response to stress / PERK-mediated unfolded protein response / methionyl-initiator methionine tRNA binding / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / cytoplasmic translational initiation / regulation of translational initiation in response to stress / translation factor activity, RNA binding / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / protein-synthesizing GTPase / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translation initiation complex formation / Response of EIF2AK4 (GCN2) to amino acid deficiency / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / mitophagy / translation initiation factor binding / translation initiation factor activity / stress granule assembly / cellular response to amino acid starvation / response to endoplasmic reticulum stress / translational initiation / PKR-mediated signaling / ABC-family proteins mediated transport / male gonad development / cytoplasmic stress granule / cellular response to UV / ribosome binding / cellular response to heat / cellular response to oxidative stress / in utero embryonic development / cadherin binding / GTPase activity / mRNA binding / synapse / GTP binding / mitochondrion / RNA binding / extracellular exosome / zinc ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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 / 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 ...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 / 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 / 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 elongation factor EF1A/initiation factor IF2gamma, C-terminal / S1 domain profile. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Translation protein, beta-barrel domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Eukaryotic translation initiation factor 2 subunit 1 / Eukaryotic translation initiation factor 2 subunit 2 / Eukaryotic translation initiation factor 2 subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBrito Querido J / Sokabe M
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
CitationJournal: Science / Year: 2020
Title: Structure of a human 48 translational initiation complex.
Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan /
Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning.
History
DepositionMar 17, 2020-
Header (metadata) releaseSep 16, 2020-
Map releaseSep 16, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ybv
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10774.png

Downloads & links

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Map

FileDownload / File: emd_10774.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 500 pix.
= 537. Å		1.07 Å/pix.
x 500 pix.
= 537. Å		1.07 Å/pix.
x 500 pix.
= 537. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.035
Minimum - Maximum-0.13308457 - 0.23474605
Average (Standard dev.)0.00015950525 (±0.0037637458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 537.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z537.000537.000537.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.1330.2350.000

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Supplemental data

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Mask #1

Fileemd_10774_msk_1.map
Projections & Slices
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Additional map: #1

Fileemd_10774_additional.map
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Half map: #1

Fileemd_10774_half_map_1.map
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Half map: #2

Fileemd_10774_half_map_2.map
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Sample components

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Entire : 48S initiation complex

EntireName: 48S initiation complex
Components
  • Complex: 48S initiation complex
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 2
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 1
    • RNA: Initiator methionine tRNA
    • RNA: mRNA
    • Protein or peptide: Eukaryotic translation initiation factor 2 subunit 3

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Supramolecule #1: 48S initiation complex

SupramoleculeName: 48S initiation complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Eukaryotic translation initiation factor 2 subunit 2

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.454484 KDa
SequenceString: MSGDEMIFDP TMSKKKKKKK KPFMLDEEGD TQTEETQPSE TKEVEPEPTE DKDLEADEED TRKKDASDDL DDLNFFNQKK KKKKTKKIF DIDEAEEGVK DLKIESDVQE PTEPEDDLDI MLGNKKKKKK NVKFPDEDEI LEKDEALEDE DNKKDDGISF S NQTGPAWA ...String:
MSGDEMIFDP TMSKKKKKKK KPFMLDEEGD TQTEETQPSE TKEVEPEPTE DKDLEADEED TRKKDASDDL DDLNFFNQKK KKKKTKKIF DIDEAEEGVK DLKIESDVQE PTEPEDDLDI MLGNKKKKKK NVKFPDEDEI LEKDEALEDE DNKKDDGISF S NQTGPAWA GSERDYTYEE LLNRVFNIMR EKNPDMVAGE KRKFVMKPPQ VVRVGTKKTS FVNFTDICKL LHRQPKHLLA FL LAELGTS GSIDGNNQLV IKGRFQQKQI ENVLRRYIKE YVTCHTCRSP DTILQKDTRL YFLQCETCHS RCSVASIKTG FQA VTGKRA QLRAKAN

UniProtKB: Eukaryotic translation initiation factor 2 subunit 2

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Macromolecule #2: Eukaryotic translation initiation factor 2 subunit 1

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.16118 KDa
SequenceString: MPGLSCRFYQ HKFPEVEDVV MVNVRSIAEM GAYVSLLEYN NIEGMILLSE LSRRRIRSIN KLIRIGRNEC VVVIRVDKEK GYIDLSKRR VSPEEAIKCE DKFTKSKTVY SILRHVAEVL EYTKDEQLES LFQRTAWVFD DKYKRPGYGA YDAFKHAVSD P SILDSLDL ...String:
MPGLSCRFYQ HKFPEVEDVV MVNVRSIAEM GAYVSLLEYN NIEGMILLSE LSRRRIRSIN KLIRIGRNEC VVVIRVDKEK GYIDLSKRR VSPEEAIKCE DKFTKSKTVY SILRHVAEVL EYTKDEQLES LFQRTAWVFD DKYKRPGYGA YDAFKHAVSD P SILDSLDL NEDEREVLIN NINRRLTPQA VKIRADIEVA CYGYEGIDAV KEALRAGLNC STENMPIKIN LIAPPRYVMT TT TLERTEG LSVLSQAMAV IKEKIEEKRG VFNVQMEPKV VTDTDETELA RQMERLEREN AEVDGDDDAE EMEAKAED

UniProtKB: Eukaryotic translation initiation factor 2 subunit 1

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Macromolecule #5: Eukaryotic translation initiation factor 2 subunit 3

MacromoleculeName: Eukaryotic translation initiation factor 2 subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-synthesizing GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.178406 KDa
SequenceString: MAGGEAGVTL GQPHLSRQDL TTLDVTKLTP LSHEVISRQA TINIGTIGHV AHGKSTVVKA ISGVHTVRFK NELERNITIK LGYANAKIY KLDDPSCPRP ECYRSCGSST PDEFPTDIPG TKGNFKLVRH VSFVDCPGHD ILMATMLNGA AVMDAALLLI A GNESCPQP ...String:
MAGGEAGVTL GQPHLSRQDL TTLDVTKLTP LSHEVISRQA TINIGTIGHV AHGKSTVVKA ISGVHTVRFK NELERNITIK LGYANAKIY KLDDPSCPRP ECYRSCGSST PDEFPTDIPG TKGNFKLVRH VSFVDCPGHD ILMATMLNGA AVMDAALLLI A GNESCPQP QTSEHLAAIE IMKLKHILIL QNKIDLVKES QAKEQYEQIL AFVQGTVAEG APIIPISAQL KYNIEVVCEY IV KKIPVPP RDFTSEPRLI VIRSFDVNKP GCEVDDLKGG VAGGSILKGV LKVGQEIEVR PGIVSKDSEG KLMCKPIFSK IVS LFAEHN DLQYAAPGGL IGVGTKIDPT LCRADRMVGQ VLGAVGALPE IFTELEISYF LLRRLLGVRT EGDKKAAKVQ KLSK NEVLM VNIGSLSTGG RVSAVKADLG KIVLTNPVCT EVGEKIALSR RVEKHWRLIG WGQIRRGVTI KPTVDDD

UniProtKB: Eukaryotic translation initiation factor 2 subunit 3

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Macromolecule #3: Initiator methionine tRNA

MacromoleculeName: Initiator methionine tRNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.23151 KDa
SequenceString:
AGCAGAGUGG CGCAGCGGAA GCGUGCUGGG CCCAUAACCC AGAGGUCGAU GGAUCGAAAC CAUCCUCUGC UACCA

GENBANK: GENBANK: K00328.1

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Macromolecule #4: mRNA

MacromoleculeName: mRNA / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 942.66 Da
SequenceString:
AAA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 107.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4kzy

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 33706
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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