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 1.0 of the entry. See complete history. 


Literature

Structural insights into inactive ribosome complexes derived from cold-treated chick embryo cells

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

To be published.

Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41D [auth Az]25Gallus gallusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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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
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30J [auth BF]246Gallus gallusMutation(s): 0 
UniProt
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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
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal 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 
UniProt
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
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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
60S ribosomal protein L17S [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 
UniProt
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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 
UniProt
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 
UniProt
Find proteins for Q98TF6 (Gallus gallus)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37MA [auth Bj]97Gallus gallusMutation(s): 0 
UniProt
Find proteins for E1C810 (Gallus gallus)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38NA [auth Bk]70Gallus gallusMutation(s): 0 
UniProt
Find proteins for E1BU66 (Gallus gallus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39OA [auth Bl]51Gallus gallusMutation(s): 0 
UniProt
Find proteins for Q98TF5 (Gallus gallus)
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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
Find proteins for P32046 (Gallus gallus)
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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
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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
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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
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S7GB [auth Ag]194Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29HB [auth AG]171Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S8IB [auth Ah]207Gallus gallusMutation(s): 0 
UniProt
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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
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15NB [auth Am]151Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S14OB [auth An]151Gallus gallusMutation(s): 0 
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
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17QB [auth Aq]135Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18RB [auth Ar]152Gallus gallusMutation(s): 0 
UniProt
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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
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein eS21UB [auth Au]83Gallus gallusMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15aVB [auth Av]130Gallus gallusMutation(s): 0 
UniProt
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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
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25YB [auth Ay]125Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2ZB [auth AZ]296Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein S16AC [auth Ap]146Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
SERPINE1 mRNA binding protein 1CC [auth S]404Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2DC [auth A]858Gallus gallusMutation(s): 0 
EC: 3.6.5
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL10EC [auth Bs]316Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L12FC [auth Bt]165Gallus gallusMutation(s): 0 
UniProt
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal proteinGC [auth Bv]217Gallus gallusMutation(s): 0 
UniProt
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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  5 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
SAC
Query on SAC		ZB [auth AZ]L-PEPTIDE LINKINGC5 H9 N O4SER
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