8BTK

Structure of the TRAP complex with the Sec translocon and a translating ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.1 of the entry. See complete history. 


Literature

Molecular basis of the TRAP complex function in ER protein biogenesis.

Jaskolowski, M., Jomaa, A., Gamerdinger, M., Shrestha, S., Leibundgut, M., Deuerling, E., Ban, N.

(2023) Nat Struct Mol Biol 30: 770-777

  • DOI: https://doi.org/10.1038/s41594-023-00990-0
  • Primary Citation of Related Structures:  
    8BTK

  • PubMed Abstract: 

    The translocon-associated protein (TRAP) complex resides in the endoplasmic reticulum (ER) membrane and interacts with the Sec translocon and the ribosome to facilitate biogenesis of secretory and membrane proteins. TRAP plays a key role in the secretion of many hormones, including insulin. Here we reveal the molecular architecture of the mammalian TRAP complex and how it engages the translating ribosome associated with Sec61 translocon on the ER membrane. The TRAP complex is anchored to the ribosome via a long tether and its position is further stabilized by a finger-like loop. This positions a cradle-like lumenal domain of TRAP below the translocon for interactions with translocated nascent chains. Our structure-guided TRAP mutations in Caenorhabditis elegans lead to growth deficits associated with increased ER stress and defects in protein hormone secretion. These findings elucidate the molecular basis of the TRAP complex in the biogenesis and translocation of proteins at the ER.

    • Organizational Affiliation: 

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8D [auth BA]257Oryctolagus cuniculusMutation(s): 0 
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UniProt GroupsA0A5F9C4D3A0A5F9D5B2
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3E [auth BB]403Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4F [auth BC]413Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18_c domain-containing proteinG [auth BD]297Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6H [auth BE]291Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
uL30,60S ribosomal protein L7I [auth BF]247Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aJ [auth BG]266Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9K [auth BH]192Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10L [auth BI]214Oryctolagus cuniculusMutation(s): 0 
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Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L11M [auth BJ]178Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Nascent chainN [auth BK]29Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
L13O [auth BL]211Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TKB3 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L14P [auth BM]218Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth BN]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aR [auth BO]203Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A0N8ETI8 (Heterocephalus glaber)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
uL22S [auth BP]184Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
eL18T [auth BQ]188Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for F6QKI9 (Callithrix jacchus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19U [auth BR]196Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aV [auth BS]176Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTY7 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21W [auth BT]160Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22X [auth BU]128Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L23Y [auth BV]140Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth BW]157Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L23eN domain-containing proteinAA [auth BX]156Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26BA [auth BY]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27CA [auth BZ]136Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aDA [auth Ba]148Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth Bb]245Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
eL30FA [auth Bc]115Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L31GA [auth Bd]125Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL32HA [auth Be]135Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aIA [auth Bf]110Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34JA [auth Bg]117Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35KA [auth Bh]123Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36LA [auth Bi]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37MA [auth Bj]97Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
eL38NA [auth Bk]70Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
eL39OA [auth Bl]51Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinPA [auth Bm]128Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P62975 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL42QA [auth Bo]106Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL43RA [auth Bp]92Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28SA [auth Br]137Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0TA [auth Bs]318Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SPK4 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L12UA [auth Bt]165Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL1VA [auth Bv]217Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1WA [auth SX]476Canis lupus familiarisMutation(s): 0 
UniProt
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaXA [auth SY]68Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P60058 (Canis lupus familiaris)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit betaYA [auth SZ]96Canis lupus familiarisMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27AB [auth AA]84Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S28BB [auth AB]69Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TIB4 (Oryctolagus cuniculus)
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S27aCB [auth AC]156Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30DB [auth AD]133Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
eS26EB [auth AE]115Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A2K5LQY6 (Cercocebus atys)
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1FB [auth AF]317Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
uS14GB [auth AG]56Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAJB [auth AZ]295Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aKB [auth Aa]264Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_S5_C domain-containing protein,40S ribosomal protein S2LB [auth Ab]293Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9D8I1 (Oryctolagus cuniculus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3MB [auth Ac]281Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4NB [auth Ad]263Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5OB [auth Ae]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S6PB [auth Af]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7QB [auth Ag]432Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8RB [auth Ah]208Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S9 (Predicted)SB [auth Ai]194Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS10TB [auth Aj]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11UB [auth Ak]158Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12VB [auth Al]132Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
uS15WB [auth Am]151Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14XB [auth An]151Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS19YB [auth Ao]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
uS9ZB [auth Ap]172Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein eS17AC [auth Aq]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TU13 (Oryctolagus cuniculus)
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18BC [auth Ar]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19CC [auth As]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein uS10DC [auth At]119Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21EC [auth Au]83Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S15aFC [auth Av]130Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23GC [auth Aw]143Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24HC [auth Ax]130Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 87
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25IC [auth Ay]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 88
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41JC [auth Az]25Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 89
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit alphaKC [auth TA]286Canis lupus familiarisMutation(s): 0 
UniProt
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Entity ID: 90
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit betaLC [auth TB]183Canis lupus familiarisMutation(s): 0 
UniProt
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Entity ID: 91
MoleculeChains Sequence LengthOrganismDetailsImage
Signal sequence receptor subunit 3MC [auth TC]185Canis lupus familiarisMutation(s): 0 
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Entity ID: 92
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit deltaNC [auth TD]173Canis lupus familiarisMutation(s): 0 
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
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BX [auth B7]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
SPM
Query on SPM
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BD [auth B5],
YC [auth B5],
YZ [auth A2]		SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD
Query on SPD
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AD [auth B5]
CD [auth B5]
DD [auth B5]
ED [auth B5]
FD [auth B5]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
AAC
Query on AAC
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PY [auth BD]ACETYLAMINO-ACETIC ACID
C4 H7 N O3
OKJIRPAQVSHGFK-UHFFFAOYSA-N
ZN
Query on ZN
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IZ [auth Bg]
JZ [auth Bj]
KGA [auth AC]
LGA [auth AE]
MGA [auth AG]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AAA [auth A2]
ABA [auth A2]
ACA [auth A2]
ADA [auth A2]
AE [auth B5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  8 Unique
IDChains TypeFormula2D DiagramParent
V5N
Query on V5N		D [auth BA]L-PEPTIDE LINKINGC6 H9 N3 O3HIS
HIC
Query on HIC		E [auth BB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
AYA
Query on AYA		F [auth BC]L-PEPTIDE LINKINGC5 H9 N O3ALA
MLZ
Query on MLZ		EA [auth Bb]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
M3L
Query on M3L		PA [auth Bm]L-PEPTIDE LINKINGC9 H21 N2 O2LYS
SAC
Query on SAC		SA [auth Br]L-PEPTIDE LINKINGC5 H9 N O4SER
NMM
Query on NMM		CC [auth As]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
HY3
Query on HY3		GC [auth Aw]L-PEPTIDE LINKINGC5 H9 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.4

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland310030B_163478
Swiss National Science FoundationSwitzerland51NF40_141735

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-24
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2024-04-24
    Changes: Data collection, Structure summary