6FEC

Human cap-dependent 48S pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a human cap-dependent 48S translation pre-initiation complex.

Eliseev, B.Yeramala, L.Leitner, A.Karuppasamy, M.Raimondeau, E.Huard, K.Alkalaeva, E.Aebersold, R.Schaffitzel, C.

(2018) Nucleic Acids Res 46: 2678-2689

  • DOI: 10.1093/nar/gky054
  • Primary Citation of Related Structures:  
    6FEC

  • PubMed 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 the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA ...

    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.


    Organizational Affiliation

    School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit A11362Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit C2843Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit E3445Homo sapiensMutation(s): 0 
Gene Names: EIF3EEIF3S6INT6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit F4364Homo sapiensMutation(s): 0 
EC: 3.4.19.12
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit H5352Homo sapiensMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit K6218Homo sapiensMutation(s): 0 
Gene Names: EIF3KEIF3S12ARG134HSPC029MSTP001PTD001
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PHAROS  Q9UBQ5
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit L7564Homo sapiensMutation(s): 0 
Gene Names: EIF3LEIF3EIPEIF3S6IPHSPC021HSPC025MSTP005
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PHAROS  Q9Y262
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit M8374Homo sapiensMutation(s): 0 
Gene Names: EIF3MHFLB5PCID1GA17PNAS-125
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D9368Homo sapiensMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S11G158Homo sapiensMutation(s): 0 
Gene Names: RPS11
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S16H141Homo sapiensMutation(s): 0 
Gene Names: RPS16
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4, X isoformI263Homo sapiensMutation(s): 0 
Gene Names: RPS4XCCG2RPS4SCAR
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Entity ID: 15
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40S ribosomal protein S29J53Homo sapiensMutation(s): 0 
Gene Names: RPS29
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Entity ID: 16
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40S ribosomal protein S9K182Homo sapiensMutation(s): 0 
Gene Names: RPS9
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S18L137Homo sapiensMutation(s): 0 
Gene Names: RPS18D6S218E
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 2 subunit 1P266Homo sapiensMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23Q142Homo sapiensMutation(s): 0 
Gene Names: RPS23
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S19R141Homo sapiensMutation(s): 0 
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Entity ID: 22
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Eukaryotic translation initiation factor 2 subunit 3S422Homo sapiensMutation(s): 0 
Gene Names: EIF2S3EIF2G
EC: 3.6.5.3
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Entity ID: 23
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40S ribosomal protein S5U191Homo sapiensMutation(s): 0 
Gene Names: RPS5
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Entity ID: 24
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40S ribosomal protein S30V59Homo sapiensMutation(s): 0 
Gene Names: FAU
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Entity ID: 25
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40S ribosomal protein S25W75Homo sapiensMutation(s): 0 
Gene Names: RPS25
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Entity ID: 26
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40S ribosomal protein S7X190Homo sapiensMutation(s): 0 
Gene Names: RPS7
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S27Y84Homo sapiensMutation(s): 0 
Gene Names: RPS27MPS1
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S13Z150Homo sapiensMutation(s): 0 
Gene Names: RPS13
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S15aa129Homo sapiensMutation(s): 0 
Gene Names: RPS15AOK/SW-cl.82
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Entity ID: 30
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40S ribosomal protein S21b82Homo sapiensMutation(s): 0 
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Entity ID: 31
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40S ribosomal protein S2c226Homo sapiensMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)d17Homo sapiensMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S17e126Homo sapiensMutation(s): 0 
Gene Names: RPS17RPS17L
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein SAf208Homo sapiensMutation(s): 0 
Gene Names: RPSALAMBRLAMR1
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3g227Homo sapiensMutation(s): 0 
Gene Names: RPS3OK/SW-cl.26
EC: 4.2.99.18
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S20h104Homo sapiensMutation(s): 0 
Gene Names: RPS20
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3ai215Homo sapiensMutation(s): 0 
Gene Names: RPS3AFTE1MFTL
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Entity ID: 38
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40S ribosomal protein S14j136Homo sapiensMutation(s): 0 
Gene Names: RPS14PRO2640
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Entity ID: 39
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40S ribosomal protein S26k99Homo sapiensMutation(s): 0 
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Entity ID: 40
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40S ribosomal protein S28l64Homo sapiensMutation(s): 0 
Gene Names: RPS28
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Receptor of activated protein C kinase 1m313Homo sapiensMutation(s): 0 
Gene Names: RACK1GNB2L1HLC7PIG21
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Entity ID: 42
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40S ribosomal protein S15n127Homo sapiensMutation(s): 0 
Gene Names: RPS15RIG
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Entity ID: 43
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40S ribosomal protein S8o206Homo sapiensMutation(s): 0 
Gene Names: RPS8OK/SW-cl.83
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Entity ID: 44
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Ubiquitin-40S ribosomal protein S27ap71Homo sapiensMutation(s): 0 
Gene Names: RPS27AUBA80UBCEP1
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6q237Homo sapiensMutation(s): 0 
Gene Names: RPS6OK/SW-cl.2
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S12r124Homo sapiensMutation(s): 0 
Gene Names: RPS12
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Entity ID: 47
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40S ribosomal protein S24s131Homo sapiensMutation(s): 0 
Gene Names: RPS24
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S10t98Homo sapiensMutation(s): 0 
Gene Names: RPS10
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4Bu636Homo sapiensMutation(s): 0 
Gene Names: EIF4B
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 3 subunit Bw1121Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChainsLengthOrganismImage
18S ribosomal RNAA1776Homo sapiens
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Entity ID: 11
MoleculeChainsLengthOrganismImage
Messenger RNA (26-MER)F26Homo sapiens
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Entity ID: 18
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Transfer RNA (75-MER)N75Homo sapiens
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilBelgium281331
EMBL-RFBRBelgium15-54-74001

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-03
    Changes: Data collection, Refinement description