8VVT | pdb_00008vvt

Mammalian ribosomes bound to Anisomycin in the rotated conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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

Rapid purification reveals structural insights into transient ribosome states

Loerch, S.Petrossian, E.Smith, P.R.Campbell, Z.T.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L8257Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TT27 (Oryctolagus cuniculus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
uL3403Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TL06 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
uL4425Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9C3C5 (Oryctolagus cuniculus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
L5297Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
L6291Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
uL30247Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB1 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
eL8319Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1STW0 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
uL6192Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SWI6 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
L10214Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for B7NZQ2 (Oryctolagus cuniculus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
L11178Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
L14K [auth L]218Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SZ12 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
L15L [auth M]204Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T0C1 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
uL13M [auth N]203Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
uL22N [auth O]184Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
eL18O [auth P]188Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TFE0 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
eL19P [auth Q]196Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TJR3 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
eL20Q [auth R]176Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTY7 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
eL21R [auth S]160Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
eL22S [auth T]128Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TSG1 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
L23T [auth U]140Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
L24U [auth V]157Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
uL23V [auth W]156Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
L26W [auth X]145Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SQH0 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
L27X [auth Y]136Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
uL15Y [auth Z]148Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SNY0 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
eL13Z [auth K]211Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TPV0 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
uS2AA [auth AB]295Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TLT8 (Oryctolagus cuniculus)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
S3ABA [auth BB]264Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SS70 (Oryctolagus cuniculus)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
eS1CA [auth CB]293Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
eL29GA [auth AA]245Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
eL30HA [auth BA]115Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
eL31IA [auth CA]125Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SHG0 (Oryctolagus cuniculus)
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL32JA [auth DA]135Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL33KA [auth EA]110Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SF08 (Oryctolagus cuniculus)
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
eL34LA [auth FA]117Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TXG5 (Oryctolagus cuniculus)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
uL29MA [auth GA]123Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SIT5 (Oryctolagus cuniculus)
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
L36NA [auth HA]105Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTQ5 (Oryctolagus cuniculus)
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
L37OA [auth IA]97Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for U3KPD5 (Oryctolagus cuniculus)
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
eL38PA [auth JA]70Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
eL39QA [auth KA]51Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
eL40RA [auth LA]102Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
eL41SA [auth MA]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
eL42TA [auth NA]106Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
eL43UA [auth OA]92Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SY53 (Oryctolagus cuniculus)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
eL28VA [auth PA]137Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1U7L1 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
uL10WA [auth QA]318Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SPK4 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
uL3XA [auth RA]165Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SMR7 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
eukaryotic elongation factor 2YA [auth v]839Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Serpine mRNA binding protein 1ZA [auth w]46Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
uS3BB [auth DB]243Oryctolagus cuniculusMutation(s): 0 
EC: 4.2.99.18
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
eS4CB [auth EB]263Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TK17 (Oryctolagus cuniculus)
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
S5DB [auth FB]204Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
S6EB [auth GB]249Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
S7FB [auth HB]194Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
eS8GB [auth IB]208Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TJW1 (Oryctolagus cuniculus)
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
S9HB [auth JB]194Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
eS10IB [auth KB]165Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
S11JB [auth LB]158Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
S12KB [auth MB]132Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
uS15LB [auth NB]151Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
uS11MB [auth OB]168Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
uS19NB [auth PB]145Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
S16OB [auth QB]146Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
eS17PB [auth RB]135Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
uS13QB [auth SB]152Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
eS19RB [auth TB]145Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
uS10SB [auth UB]119Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
eS21TB [auth VB]83Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
S15AUB [auth WB]130Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
uS12VB [auth XB]143Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
eS24WB [auth YB]130Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
eS25XB [auth ZB]125Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
eS26YB [auth AC]115Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TFE8 (Oryctolagus cuniculus)
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
S27ZB [auth BC]84Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TZ76 (Oryctolagus cuniculus)
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
S28AC [auth CC]69Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
uS14BC [auth DC]56Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
S30CC [auth EC]133Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T8A2 (Oryctolagus cuniculus)
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
S27ADC [auth FC]156Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
RACK1EC [auth GC]317Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
Proliferation-associated protein 2G4FC [auth b]394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 30
MoleculeChains LengthOrganismImage
28S rRNADA [auth WA]3,635Oryctolagus cuniculus
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Entity ID: 31
MoleculeChains LengthOrganismImage
5S rRNAEA [auth XA]120Oryctolagus cuniculus
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Entity ID: 32
MoleculeChains LengthOrganismImage
5.8S rRNAFA [auth YA]156Oryctolagus cuniculus
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Entity ID: 53
MoleculeChains LengthOrganismImage
18S rRNAAB [auth ZA]1,869Oryctolagus cuniculus
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
GH [auth v]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ANM
Query on ANM

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FG [auth WA]ANISOMYCIN
C14 H19 N O4
YKJYKKNCCRKFSL-RDBSUJKOSA-N
SPD
Query on SPD

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GG [auth WA]SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN
Query on ZN

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BH [auth IA]
CI [auth AC]
DH [auth LA]
DI [auth DC]
EH [auth NA]
BH [auth IA],
CI [auth AC],
DH [auth LA],
DI [auth DC],
EH [auth NA],
EI [auth FC],
FH [auth OA],
ZG [auth FA]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AD [auth WA]
AE [auth WA]
AF [auth WA]
AG [auth WA]
AH [auth FA]
AD [auth WA],
AE [auth WA],
AF [auth WA],
AG [auth WA],
AH [auth FA],
AI [auth TB],
BD [auth WA],
BE [auth WA],
BF [auth WA],
BG [auth WA],
BI [auth AC],
CD [auth WA],
CE [auth WA],
CF [auth WA],
CG [auth WA],
CH [auth KA],
DD [auth WA],
DE [auth WA],
DF [auth WA],
DG [auth WA],
ED [auth WA],
EE [auth WA],
EF [auth WA],
EG [auth WA],
FD [auth WA],
FE [auth WA],
FF [auth WA],
GC [auth B],
GD [auth WA],
GE [auth WA],
GF [auth WA],
HC [auth B],
HD [auth WA],
HE [auth WA],
HF [auth WA],
HG [auth WA],
HH [auth ZA],
IC [auth I],
ID [auth WA],
IE [auth WA],
IF [auth WA],
IG [auth WA],
IH [auth ZA],
JC [auth O],
JD [auth WA],
JE [auth WA],
JF [auth WA],
JG [auth WA],
JH [auth ZA],
KC [auth U],
KD [auth WA],
KE [auth WA],
KF [auth WA],
KG [auth WA],
KH [auth ZA],
LC [auth WA],
LD [auth WA],
LE [auth WA],
LF [auth WA],
LG [auth WA],
LH [auth ZA],
MC [auth WA],
MD [auth WA],
ME [auth WA],
MF [auth WA],
MG [auth WA],
MH [auth ZA],
NC [auth WA],
ND [auth WA],
NE [auth WA],
NF [auth WA],
NG [auth WA],
NH [auth ZA],
OC [auth WA],
OD [auth WA],
OE [auth WA],
OF [auth WA],
OG [auth WA],
OH [auth ZA],
PC [auth WA],
PD [auth WA],
PE [auth WA],
PF [auth WA],
PG [auth WA],
PH [auth ZA],
QC [auth WA],
QD [auth WA],
QE [auth WA],
QF [auth WA],
QG [auth WA],
QH [auth ZA],
RC [auth WA],
RD [auth WA],
RE [auth WA],
RF [auth WA],
RG [auth WA],
RH [auth ZA],
SC [auth WA],
SD [auth WA],
SE [auth WA],
SF [auth WA],
SG [auth WA],
SH [auth ZA],
TC [auth WA],
TD [auth WA],
TE [auth WA],
TF [auth WA],
TG [auth XA],
TH [auth ZA],
UC [auth WA],
UD [auth WA],
UE [auth WA],
UF [auth WA],
UG [auth XA],
UH [auth ZA],
VC [auth WA],
VD [auth WA],
VE [auth WA],
VF [auth WA],
VG [auth XA],
VH [auth ZA],
WC [auth WA],
WD [auth WA],
WE [auth WA],
WF [auth WA],
WG [auth XA],
WH [auth ZA],
XC [auth WA],
XD [auth WA],
XE [auth WA],
XF [auth WA],
XG [auth YA],
XH [auth ZA],
YC [auth WA],
YD [auth WA],
YE [auth WA],
YF [auth WA],
YG [auth DA],
YH [auth ZA],
ZC [auth WA],
ZD [auth WA],
ZE [auth WA],
ZF [auth WA],
ZH [auth ZA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
C
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
DDE
Query on DDE
YA [auth v]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5127
RECONSTRUCTIONcisTEM

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM146862

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-30
    Type: Initial release