8Q87

Structure of the G. gallus 80S rotated ribosome in complex with eEF2 and SERBP1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Cryo-EM structure of the inactive ribosome complex accumulated in chick embryo cells in cold-stress conditions.

Nurullina, L., Terrosu, S., Myasnikov, A.G., Jenner, L.B., Yusupov, M.

(2024) FEBS Lett 598: 537-547

  • DOI: https://doi.org/10.1002/1873-3468.14831
  • Primary Citation of Related Structures:  
    8Q7Z, 8Q87

  • PubMed Abstract: 

    Here, we present the high-resolution structure of the Gallus gallus 80S ribosome obtained from cold-treated chicken embryos. The translationally inactive ribosome complex contains elongation factor eEF2 with GDP, SERPINE1 mRNA binding protein 1 (SERBP1) and deacylated tRNA in the P/E position, showing common features with complexes already described in mammals. Modeling of most expansion segments of G. gallus 28S ribosomal RNA allowed us to identify specific features in their structural organization and to describe areas where a marked difference between mammalian and avian ribosomes could shed light on the evolution of the expansion segments. This study provides the first structure of an avian ribosome, establishing a model for future structural and functional studies on the translational machinery in Aves.

    • Organizational Affiliation: 

    Integrated Structural Biology, IGBMC - IGBMC - CNRS UMR 7104, Inserm, France.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41D [auth Az]25Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8E [auth BA]257Gallus gallusMutation(s): 0 
UniProt
Find proteins for F1NIX0 (Gallus gallus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL3F [auth BB]403Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4 C-terminal domain-containing proteinG [auth BC]421Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q5ZII1 (Gallus gallus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18H [auth BD]297Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6I [auth BE]298Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q8UWG7 (Gallus gallus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30J [auth BF]246Gallus gallusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8K [auth BG]266Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9L [auth BH]192Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A1D5NVI1 (Gallus gallus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL16,Large ribosomal subunit protein uL16,Large ribosomal subunit protein uL16,Large ribosomal subunit protein uL16,Large ribosomal subunit protein uL16M [auth BI]214Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q08200 (Gallus gallus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11N [auth BJ]178Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A1D5P3B1 (Gallus gallus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13O [auth BL]211Gallus gallusMutation(s): 0 
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Find proteins for P41125 (Gallus gallus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14P [auth BM]131Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q98TF9 (Gallus gallus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15Q [auth BN]204Gallus gallusMutation(s): 0 
UniProt
Find proteins for F1NQG5 (Gallus gallus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL13R [auth BO]203Gallus gallusMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22S [auth BP]184Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A1D5PR40 (Gallus gallus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL18T [auth BQ]187Gallus gallusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19U [auth BR]196Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q5ZKK8 (Gallus gallus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL20V [auth BS]176Gallus gallusMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21W [auth BT]160Gallus gallusMutation(s): 0 
UniProt
Find proteins for R4GIQ2 (Gallus gallus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL22X [auth BU]128Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q98TF8 (Gallus gallus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protei uL14Y [auth BV]140Gallus gallusMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24Z [auth BW]157Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A8V0XRE7 (Gallus gallus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL23AA [auth BX]155Gallus gallusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26 like 1BA [auth BY]145Gallus gallusMutation(s): 0 
UniProt
Find proteins for F2Z4K6 (Gallus gallus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL27CA [auth BZ]136Gallus gallusMutation(s): 0 
UniProt
Find proteins for P61355 (Gallus gallus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uL15DA [auth Ba]148Gallus gallusMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth Bb]71Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A1L1RNZ2 (Gallus gallus)
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30FA [auth Bc]115Gallus gallusMutation(s): 0 
UniProt
Find proteins for P67883 (Gallus gallus)
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31GA [auth Bd]176Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A1L1RT94 (Gallus gallus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32HA [auth Be]135Gallus gallusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eL33IA [auth Bf]110Gallus gallusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34JA [auth Bg]117Gallus gallusMutation(s): 0 
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Find proteins for A0A1L1S0X5 (Gallus gallus)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29KA [auth Bh]123Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q98TF7 (Gallus gallus)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL36LA [auth Bi]105Gallus gallusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37MA [auth Bj]97Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38NA [auth Bk]70Gallus gallusMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39OA [auth Bl]51Gallus gallusMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40PA [auth Bm]128Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L36a likeQA [auth Bo]105Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43RA [auth Bp]92Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28SA [auth Br]138Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS1UA [auth Aa]264Gallus gallusMutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27VA [auth AA]84Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A3Q2TV39 (Gallus gallus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S28WA [auth AB]69Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A3Q2U825 (Gallus gallus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S2XA [auth Ab]264Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A8V0Z891 (Gallus gallus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinYA [auth AC]156Gallus gallusMutation(s): 0 
UniProt
Find proteins for P79781 (Gallus gallus)
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-(apurinic or apyrimidinic site) lyaseZA [auth Ac]243Gallus gallusMutation(s): 0 
EC: 4.2.99.18
UniProt
Find proteins for F1NPA9 (Gallus gallus)
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4AB [auth Ad]263Gallus gallusMutation(s): 0 
UniProt
Find proteins for P47836 (Gallus gallus)
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS30BB [auth AD]133Gallus gallusMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26CB [auth AE]115Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q5ZM66 (Gallus gallus)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S5DB [auth Ae]204Gallus gallusMutation(s): 0 
UniProt
Find proteins for G1TFM5 (Oryctolagus cuniculus)
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6EB [auth Af]249Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein RACK1FB [auth AF]317Gallus gallusMutation(s): 0 
UniProt
Find proteins for P63247 (Gallus gallus)
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7GB [auth Ag]194Gallus gallusMutation(s): 0 
UniProt
Find proteins for F1NN16 (Gallus gallus)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29HB [auth AG]171Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A8V0Z8V3 (Gallus gallus)
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8IB [auth Ah]207Gallus gallusMutation(s): 0 
UniProt
Find proteins for F1NB02 (Gallus gallus)
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S9JB [auth Ai]194Gallus gallusMutation(s): 0 
UniProt
Find proteins for B7NZS8 (Oryctolagus cuniculus)
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S10KB [auth Aj]165Gallus gallusMutation(s): 0 
UniProt
Find proteins for E1C4N0 (Gallus gallus)
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11LB [auth Ak]158Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q98TH5 (Gallus gallus)
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS12MB [auth Al]132Gallus gallusMutation(s): 0 
UniProt
Find proteins for P84175 (Gallus gallus)
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15NB [auth Am]151Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q6ITC7 (Gallus gallus)
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14OB [auth An]151Gallus gallusMutation(s): 1 
UniProt
Find proteins for Q5ZHW8 (Gallus gallus)
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19PB [auth Ao]145Gallus gallusMutation(s): 0 
UniProt
Find proteins for P62846 (Gallus gallus)
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17QB [auth Aq]135Gallus gallusMutation(s): 0 
UniProt
Find proteins for P08636 (Gallus gallus)
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18RB [auth Ar]152Gallus gallusMutation(s): 0 
UniProt
Find proteins for G1TPG3 (Oryctolagus cuniculus)
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS19SB [auth As]145Gallus gallusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20TB [auth At]119Gallus gallusMutation(s): 0 
UniProt
Find proteins for F1NH93 (Gallus gallus)
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS21UB [auth Au]84Gallus gallusMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aVB [auth Av]130Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A3Q3A7P6 (Gallus gallus)
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein uS12WB [auth Aw]143Gallus gallusMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24XB [auth Ax]131Gallus gallusMutation(s): 0 
UniProt
Find proteins for F1NF89 (Gallus gallus)
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25YB [auth Ay]125Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A8V1A7V4 (Gallus gallus)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2ZB [auth AZ]296Gallus gallusMutation(s): 1 
UniProt
Find proteins for P50890 (Gallus gallus)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16AC [auth Ap]146Gallus gallusMutation(s): 0 
UniProt
Find proteins for R4GGJ0 (Gallus gallus)
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
SERPINE1 mRNA binding protein 1CC [auth S]404Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A8V0ZUK5 (Gallus gallus)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2DC [auth A]858Gallus gallusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q90705 (Gallus gallus)
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10EC [auth Bs]316Gallus gallusMutation(s): 0 
UniProt
Find proteins for P47826 (Gallus gallus)
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12FC [auth Bt]165Gallus gallusMutation(s): 0 
UniProt
Find proteins for E1BTG1 (Gallus gallus)
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinGC [auth Bv]217Gallus gallusMutation(s): 0 
UniProt
Find proteins for F6SU35 (Gallus gallus)
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
MV [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
EV [auth AC]
FV [auth AE]
HV [auth AG]
MQ [auth Bg]
NQ [auth Bj]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AD [auth B5]
AE [auth B5]
AF [auth B5]
AG [auth B5]
AH [auth B5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC		F [auth BB]L-PEPTIDE LINKINGC7 H11 N3 O2HIS
MLZ
Query on MLZ		QA [auth Bo]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
NMM
Query on NMM		SB [auth As]L-PEPTIDE LINKINGC7 H16 N4 O2ARG
DDE
Query on DDE		DC [auth A]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19rc4_4035:

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Fondation pour la Recherche Medicale (FRM)France--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-28
    Type: Initial release
  • Version 2.0: 2025-03-12
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary