9E7F

Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 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

Structure of an Archaeal Ribosome with a Divergent Active Site

Nissley, A.J.Shulgina, Y.Kivimae, R.W.Downing, B.E.Penev, P.I.Banfield, J.F.Nayak, D.D.Cate, J.H.D.

To be published.

Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Putative signal-transduction protein with CBS domainsB [auth 3]655Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MX58 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2E [auth AA]244Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MS41 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3F [auth AB]338Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4G [auth AC]285Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5H [auth AD]178Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6I [auth AE]196Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8J [auth AF]149Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13K [auth AG]186Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13L [auth AH]157Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14M [auth AI]144Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MX34 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL14N [auth AJ],
O [auth AK]
103Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MS76 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15P [auth AL]156Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eQ [auth AM]189Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MWR6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16R [auth AN]178Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18S [auth AO]205Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18T [auth AP]122Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19U [auth AQ]147Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20V [auth AR]78Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MX77 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21W [auth AS]99Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MWX9 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22X [auth AT]184Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTL6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23Y [auth AU]81Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MWI6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24Z [auth AV]128Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24AA [auth AW]62Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTA8 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29BA [auth AX]79Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTL2 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30CA [auth AY]179Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MU87 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30DA [auth AZ]101Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MXZ2 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31EA [auth Aa]91Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32FA [auth Ab]153Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34GA [auth Ac]84Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MV68 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37HA [auth Ad]52Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L38EIA [auth Ae]67Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39JA [auth Af]51Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUU4 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40KA [auth Ag]53Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MX99 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
eL42LA [auth Ah]91Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUV1 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43MA [auth Ai]102Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUM7 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
DJ-1/PfpI domain-containing proteinNA [auth Aj]184Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTM7 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
PaREP1 domain containing proteinOA [auth Ak]93Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MWU0 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS1PA [auth BA]222Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MVE0 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2QA [auth BB]208Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MS50 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3RA [auth BC]216Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTL3 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS4SA [auth BD]159Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUS9 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS4TA [auth BE]237Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MWZ7 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5UA [auth BF]202Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MU88 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS6VA [auth BG]151Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUD0 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS7WA [auth BH]223Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MS29 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS8XA [auth BI]130Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MSJ6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS8YA [auth BJ]131Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MWY2 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9ZA [auth BK]142Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MXZ8 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS10AB [auth BL]106Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MT22 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11BB [auth BM]141Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MX63 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12CB [auth BN]147Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MXZ4 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS13DB [auth BO]153Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUT0 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14EB [auth BP]54Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MSJ7 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15FB [auth BQ]151Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MVD1 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17GB [auth BR]147Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTT7 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS17HB [auth BS]71Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MS42 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19IB [auth BT]158Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTT6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS19JB [auth BU]158Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUU6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS24KB [auth BV]128Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MSX4 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S25ELB [auth BW]110Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MV37 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S26EMB [auth BX]100Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MV49 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS27NB [auth BY]67Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MUV2 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein eS28OB [auth BZ]77Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for B1Y9V2 (Pyrobaculum neutrophilum (strain DSM 2338 / JCM 9278 / NBRC 100436 / V24Sta))
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
SSU ribosomal protein S30EPB [auth Ba]54Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MSW3 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
aS35QB [auth Bb]68Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
Small zinc finger protein HVO-2753-like zinc-binding pocket domain-containing proteinRB [auth Bc]65Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MY11 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download Ideal Coordinates CCD File 
AC [auth 1]
AD [auth 1]
AK [auth 4]
BC [auth 1]
BD [auth 1]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
BO [auth BP]
CO [auth BR]
DO [auth BX]
EO [auth BY]
FO [auth Bc]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AE [auth 1]
AF [auth 1]
AG [auth 1]
AH [auth 1]
AI [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-2002182

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release