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- EMDB-10773: Structure of a human 48S translational initiation complex - eIF3bgi -

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Basic information

Entry
Database: EMDB / ID: EMD-10773
TitleStructure of a human 48S translational initiation complex - eIF3bgi
Map data
Sample
  • Complex: Eukaryotic translation initiation factor
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit AEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit IEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit BEukaryotic initiation factor 3
Function / homology
Function and homology information


viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex ...viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / IRES-dependent viral translational initiation / multi-eIF complex / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / regulation of translational initiation / 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 / translation initiation factor binding / translational initiation / translation initiation factor activity / cytoplasmic stress granule / postsynaptic density / molecular adaptor activity / mRNA binding / synapse / structural molecule activity / nucleolus / RNA binding / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor eIF2A / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain ...Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor 3 subunit A / Eukaryotic translation initiation factor eIF2A / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / WD40 repeat, conserved site / Nucleotide-binding alpha-beta plait domain superfamily / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit A
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsBrito Querido J / Sokabe M / Kraatz S / Gordiyenko Y / Skehel M / Fraser C / Ramakrishnan V
Funding support United Kingdom, United States, 3 items
OrganizationGrant numberCountry
Wellcome TrustWTY096570 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM092927 United States
Medical Research Council (MRC, United Kingdom)MC_U105184332 United Kingdom
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-
UpdateSep 16, 2020-
Current statusSep 16, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.015
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  • Surface view with fitted model
  • Atomic models: PDB-6ybt
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ybt
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10773.png

Downloads & links

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Map

FileDownload / File: emd_10773.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.074 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.06345737 - 0.15704522
Average (Standard dev.)0.00019368101 (±0.0034452998)
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-0.0630.1570.000

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Supplemental data

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Mask #1

Fileemd_10773_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: #1

Fileemd_10773_additional.map
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Half map: #2

Fileemd_10773_half_map_1.map
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Half map: #1

Fileemd_10773_half_map_2.map
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Sample components

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Entire : Eukaryotic translation initiation factor

EntireName: Eukaryotic translation initiation factor
Components
  • Complex: Eukaryotic translation initiation factor
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit AEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit IEukaryotic initiation factor 3
    • Protein or peptide: Eukaryotic translation initiation factor 3 subunit BEukaryotic initiation factor 3

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Supramolecule #1: Eukaryotic translation initiation factor

SupramoleculeName: Eukaryotic translation initiation factor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Eukaryotic translation initiation factor 3 subunit A

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 163.179531 KDa
SequenceString: DVMKSKKHRT WQKIHEPIML KYLELCVDLR KSHLAKEGLY QYKNICQQVN IKSLEDVVRA YLKMAEEKTE AAKEESQQMV LDIEDLDNI QTPESVLLSA VSGEDTQDRT DRLLLTPWVK FLWESYRQCL DLLRNNSRVE RLYHDIAQQA FKFCLQYTRK A EFRKLCDN ...String:
DVMKSKKHRT WQKIHEPIML KYLELCVDLR KSHLAKEGLY QYKNICQQVN IKSLEDVVRA YLKMAEEKTE AAKEESQQMV LDIEDLDNI QTPESVLLSA VSGEDTQDRT DRLLLTPWVK FLWESYRQCL DLLRNNSRVE RLYHDIAQQA FKFCLQYTRK A EFRKLCDN LRMHLSQIQR HHNQSTAINL NNPESQSMHL ETRLVQLDSA ISMELWQEAF KAVEDIHGLF SLSKKPPKPQ LM ANYYNKV STVFWKSGNA LFHASTLHRL YHLSREMRKN LTQDEMQRMS TRVLLATLSI PITPERTDIA RLLDMDGIIV EKQ RRLATL LGLQAPPTRI GLINDMVRFN VLQYVVPEVK DLYNWLEVEF NPLKLCERVT KVLNWVREQP EKEPELQQYV PQLQ NNTIL RLLQQVSQIY QSIEFSRLTS LVPFVDAFQL ERAIVDAARH CDLQVRIDHT SRTLSFGSDL NYATREDAPI GPHLQ SMPS EQIRNQLTAM SSVLAKALEV IKPAHILQEK EEQHQLAVTA YLKNSRKEHQ RILARRQTIE ERKERLESLN IQREKE ELE QREAELQKVR KAEEERLRQE AKEREKERIL QEHEQIKKKT VRERLEQIKK TELGAKAFKD IDIEDLEELD PDFIMAK QV EQLEKEKKEL QERLKNQEKK IDYFERAKRL EEIPLIKSAY EEQRIKDMDL WEQQEEERIT TMQLEREKAL EHKNRMSR M LEDRDLFVMR LKAARQSVYE EKLKQFEERL AEERHNRLEE RKRQRKEERR ITYYREKEEE EQRRAEEQML KEREERERA ERAKREEELR EYQERVKKLE EVERKKRQRE LEIEERERRR EEERRLGDSS LSRKDSRWGD RDSEGTWRKG PEADSEWRRG PPEKEWRRG EGRDEDRSHR RDEERPRRLG DDEDREPSLR PDDDRVPRRG MDDDRGPRRG PEEDRFSRRG ADDDRPSWRN T DDDRPPRR IADEDRGNWR HADDDRPPRR GLDEDRGSWR TADEDRGPRR GMDDDRGPRR GGADDERSSW RNADDDRGPR RG LDDDRGP RRGMDDDRGP RRGMDDDRGP RRGMDDDRGP RRGLDDDRGP WRNADDDRIP RRGAEDDRGP WRNMDDDRLS RRA DDDRFP RRGDDSRPGP WRPLVKPGGW REKEKAREES WGPPRESRPS EEREWDREKE RDRDNQDREE NDKDPERERD RERD VDRED RFRRPRDEGG WRRGPAEESS SWRDSSRRDD RDRDDRRRER DDRRDLRERR DLRDDRDRRG PPLRSEREEV SSWRR ADDR KDDRVEERDP PRRVPPPALS RDRERDRDRE REGEKEKASW RAEKDRESLR RTKNETDEDG WTTVRR

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Macromolecule #2: Eukaryotic translation initiation factor 3 subunit I

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit I / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 36.543773 KDa
SequenceString: MKPILLQGHE RSITQIKYNR EGDLLFTVAK DPIVNVWYSV NGERLGTYMG HTGAVWCVDA DWDTKHVLTG SADNSCRLWD CETGKQLAL LKTNSAVRTC GFDFGGNIIM FSTDKQMGYQ CFVSFFDLRD PSQIDNNEPY MKIPCNDSKI TSAVWGPLGE C IIAGHESG ...String:
MKPILLQGHE RSITQIKYNR EGDLLFTVAK DPIVNVWYSV NGERLGTYMG HTGAVWCVDA DWDTKHVLTG SADNSCRLWD CETGKQLAL LKTNSAVRTC GFDFGGNIIM FSTDKQMGYQ CFVSFFDLRD PSQIDNNEPY MKIPCNDSKI TSAVWGPLGE C IIAGHESG ELNQYSAKSG EVLVNVKEHS RQINDIQLSR DMTMFVTASK DNTAKLFDST TLEHQKTFRT ERPVNSAALS PN YDHVVLG GGQEAMDVTT TSTRIGKFEA RFFHLAFEEE FGRVKGHFGP INSVAFHPDG KSYSSGGEDG YVRIHYFDPQ YFE FEFEA

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Macromolecule #3: Eukaryotic translation initiation factor 3 subunit B

MacromoleculeName: Eukaryotic translation initiation factor 3 subunit B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 92.593414 KDa
SequenceString: MQDAENVAVP EAAEERAEPG QQQPAAEPPP AEGLLRPAGP GAPEAAGTEA SSEEVGIAEA GPESEVRTEP AAEAEAASGP SESPSPPAA EELPGSHAEP PVPAQGEAPG EQARDERSDS RAQAVSEDAG GNEGRAAEAE PRALENGDAD EPSFSDPEDF V DDVSEEEL ...String:
MQDAENVAVP EAAEERAEPG QQQPAAEPPP AEGLLRPAGP GAPEAAGTEA SSEEVGIAEA GPESEVRTEP AAEAEAASGP SESPSPPAA EELPGSHAEP PVPAQGEAPG EQARDERSDS RAQAVSEDAG GNEGRAAEAE PRALENGDAD EPSFSDPEDF V DDVSEEEL LGDVLKDRPQ EADGIDSVIV VDNVPQVGPD RLEKLKNVIH KIFSKFGKIT NDFYPEEDGK TKGYIFLEYA SP AHAVDAV KNADGYKLDK QHTFRVNLFT DFDKYMTISD EWDIPEKQPF KDLGNLRYWL EEAECRDQYS VIFESGDRTS IFW NDVKDP VSIEERARWT ETYVRWSPKG TYLATFHQRG IALWGGEKFK QIQRFSHQGV QLIDFSPCER YLVTFSPLMD TQDD PQAII IWDILTGHKK RGFHCESSAH WPIFKWSHDG KFFARMTLDT LSIYETPSMG LLDKKSLKIS GIKDFSWSPG GNIIA FWVP EDKDIPARVT LMQLPTRQEI RVRNLFNVVD CKLHWQKNGD YLCVKVDRTP KGTQGVVTNF EIFRMREKQV PVDVVE MKE TIIAFAWEPN GSKFAVLHGE APRISVSFYH VKNNGKIELI KMFDKQQANT IFWSPQGQFV VLAGLRSMNG ALAFVDT SD CTVMNIAEHY MASDVEWDPT GRYVVTSVSW WSHKVDNAYW LWTFQGRLLQ KNNKDRFCQL LWRPRPPTLL SQEQIKQI K KDLKKYSKIF EQKDRLSQSK ASKELVERRR TMMEDFRKYR KMAQELYMEQ KNERLELRGG VDTDELDSNV DDWEEETIE FFVTEEIIPL GNQE

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144882

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