4V5Z | pdb_00004v5z

Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structure of the Mammalian 80S Ribosome at 8.7 A Resolution

Chandramouli, P., Topf, M., Menetret, J.F., Eswar, N., Cannone, J.J., Gutell, R.R., Sali, A., Akey, C.W.

(2008) Structure 16: 535-548

  • DOI: https://doi.org/10.1016/j.str.2008.01.007
  • Primary Citation of Related Structures:  
    4V5Z

  • PubMed Abstract: 

    In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.

    • Organizational Affiliation: 

    Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.


Macromolecules

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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein RACK1I [auth Aa]317Canis lupus familiarisMutation(s): 0 
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GTEx:  ENSG00000204628 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein SAJ [auth Ab]295Canis lupus familiarisMutation(s): 0 
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PHAROS:  P08865
GTEx:  ENSG00000168028 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S3eK [auth Ac]243Canis lupus familiarisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S9eL [auth Ad]209Canis lupus familiarisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S2eM [auth Ae]179Canis lupus familiarisMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S5eN [auth Ag]204Canis lupus familiarisMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S15aeO [auth Ah]130Canis lupus familiarisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S16eP [auth Ai]146Canis lupus familiarisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S20eQ [auth Aj]119Canis lupus familiarisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S14eR [auth Ak]151Canis lupus familiarisMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S23eS [auth Al]143Canis lupus familiarisMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S18eT [auth Am]152Canis lupus familiarisMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S29eU [auth An]56Canis lupus familiarisMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S13eV [auth Ao]89Canis lupus familiarisMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S11eW [auth Aq]158Canis lupus familiarisMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S Ribosomal protein S15eX [auth As]145Canis lupus familiarisMutation(s): 0 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L8AB [auth Ba]257Canis lupus familiarisMutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L3BB [auth Bb]403Canis lupus familiarisMutation(s): 0 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L4CB [auth Bc]421Canis lupus familiarisMutation(s): 0 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L11DB [auth Bd]178Canis lupus familiarisMutation(s): 0 
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L9EB [auth Be]192Canis lupus familiarisMutation(s): 0 
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L7aFB [auth Bf]266Canis lupus familiarisMutation(s): 0 
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0GB [auth Bg]317Canis lupus familiarisMutation(s): 0 
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L10HB [auth Bh]214Canis lupus familiarisMutation(s): 0 
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L12IB [auth Bi]165Canis lupus familiarisMutation(s): 0 
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aJB [auth Bj]203Canis lupus familiarisMutation(s): 0 
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L23KB [auth Bk]140Canis lupus familiarisMutation(s): 0 
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L27aLB [auth Bl]148Canis lupus familiarisMutation(s): 0 
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L15eMB [auth Bm]204Canis lupus familiarisMutation(s): 0 
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L5NB [auth Bn]297Canis lupus familiarisMutation(s): 0 
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L18OB [auth Bo]188Canis lupus familiarisMutation(s): 0 
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L19PB [auth Bp]196Canis lupus familiarisMutation(s): 0 
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L19QB [auth B7]13Canis lupus familiarisMutation(s): 0 
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L21RB [auth Bq]160Canis lupus familiarisMutation(s): 0 
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L17SB [auth Br]184Canis lupus familiarisMutation(s): 0 
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L23aTB [auth Bs]156Canis lupus familiarisMutation(s): 0 
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L26UB [auth Bt]145Canis lupus familiarisMutation(s): 0 
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L24VB [auth Bu]157Canis lupus familiarisMutation(s): 0 
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L35WB [auth Bv]123Canis lupus familiarisMutation(s): 0 
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L35XB [auth B8]10Canis lupus familiarisMutation(s): 0 
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L7YB [auth Bw]270Canis lupus familiarisMutation(s): 0 
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L31ZB [auth Bx]125Canis lupus familiarisMutation(s): 0 
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L32AC [auth By]135Canis lupus familiarisMutation(s): 0 
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L32BC [auth B9]58Canis lupus familiarisMutation(s): 0 
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L37aCC [auth Bz]92Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0CX25
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L37eDC [auth B2]97Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP49166
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Entity ID: 83
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L39eEC [auth B3]51Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP04650
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Entity ID: 84
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L44eFC [auth B4]106Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0CX27
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Entity ID: 85
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L10aGC [auth B5]212Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0CX43
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Entity ID: 86
MoleculeChains Sequence LengthOrganismDetailsImage
60S Ribosomal protein L30eHC [auth B6]115Canis lupus familiarisMutation(s): 0 
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP14120
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Entity ID: 1
MoleculeChains LengthOrganismImage
18S Ribosomal RNAA [auth AA]1,563Canis lupus familiaris
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA Expansion segment ES3B [auth AB]35Canis lupus familiaris
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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA Expansion segment ES4C [auth AC]32Canis lupus familiaris
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA Expansion segment ES6 part ID [auth AD]42Canis lupus familiaris
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Entity ID: 5
MoleculeChains LengthOrganismImage
RNA Expansion segment ES6 part IIE [auth AE]32Canis lupus familiaris
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Entity ID: 6
MoleculeChains LengthOrganismImage
RNA Expansion segment ES9F [auth AF]31Canis lupus familiaris
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Entity ID: 7
MoleculeChains LengthOrganismImage
RNA helixG [auth AG]14Canis lupus familiaris
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Entity ID: 8
MoleculeChains LengthOrganismImage
RNA helixH [auth AH]41Canis lupus familiaris
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Entity ID: 25
MoleculeChains LengthOrganismImage
5.8S Ribosomal RNAY [auth B1]123Canis lupus familiaris
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Entity ID: 26
MoleculeChains LengthOrganismImage
28S Ribosomal RNAZ [auth B0]2,903Canis lupus familiaris
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Entity ID: 27
MoleculeChains LengthOrganismImage
RNA Expansion segment ES3AA [auth BA]21Canis lupus familiaris
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Entity ID: 28
MoleculeChains LengthOrganismImage
RNA Expansion segment ES4BA [auth BB]27Canis lupus familiaris
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Entity ID: 29
MoleculeChains LengthOrganismImage
RNA Expansion segment ES5CA [auth BC]17Canis lupus familiaris
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Entity ID: 30
MoleculeChains LengthOrganismImage
RNA Expansion segment ES7 part IDA [auth BD]16Canis lupus familiaris
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Entity ID: 31
MoleculeChains LengthOrganismImage
RNA Expansion segment ES7 part IIEA [auth BE]54Canis lupus familiaris
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Entity ID: 32
MoleculeChains LengthOrganismImage
RNA Expansion segment ES7 part IIIFA [auth BF]120Canis lupus familiaris
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Entity ID: 33
MoleculeChains LengthOrganismImage
RNA Expansion segment ES9GA [auth BG]48Canis lupus familiaris
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Entity ID: 34
MoleculeChains LengthOrganismImage
RNA Expansion segment ES12HA [auth BH]25Canis lupus familiaris
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Entity ID: 35
MoleculeChains LengthOrganismImage
RNA Expansion segment ES15 part IIA [auth BI]72Canis lupus familiaris
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Entity ID: 36
MoleculeChains LengthOrganismImage
RNA Expansion segment ES15 part IIJA [auth BJ]30Canis lupus familiaris
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Entity ID: 37
MoleculeChains LengthOrganismImage
RNA Expansion segment ES19KA [auth BK]26Canis lupus familiaris
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Entity ID: 38
MoleculeChains LengthOrganismImage
RNA Expansion segment ES20LA [auth BL]20Canis lupus familiaris
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Entity ID: 39
MoleculeChains LengthOrganismImage
RNA Expansion segment ES24MA [auth BM]19Canis lupus familiaris
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Entity ID: 40
MoleculeChains LengthOrganismImage
RNA Expansion segment ES27NA [auth BN]78Canis lupus familiaris
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Entity ID: 41
MoleculeChains LengthOrganismImage
RNA Expansion segment ES30OA [auth BO]20Canis lupus familiaris
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Entity ID: 42
MoleculeChains LengthOrganismImage
RNA Expansion segment ES31 part IPA [auth BP]15Canis lupus familiaris
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Entity ID: 43
MoleculeChains LengthOrganismImage
RNA Expansion segment ES31 part IIQA [auth BQ]30Canis lupus familiaris
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Entity ID: 44
MoleculeChains LengthOrganismImage
RNA Expansion segment ES39 part IRA [auth BR]30Canis lupus familiaris
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Entity ID: 45
MoleculeChains LengthOrganismImage
RNA Expansion segment ES39 part IISA [auth BS]38Canis lupus familiaris
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Entity ID: 46
MoleculeChains LengthOrganismImage
RNA Expansion segment ES39 part IIITA [auth BT]30Canis lupus familiaris
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Entity ID: 47
MoleculeChains LengthOrganismImage
RNA Expansion segment ES41UA [auth BU]16Canis lupus familiaris
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Entity ID: 48
MoleculeChains LengthOrganismImage
RNA Expansion segment ES9 part2VA [auth BV]22Canis lupus familiaris
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Entity ID: 49
MoleculeChains LengthOrganismImage
RNA Expansion segment ES10WA [auth BW]16Canis lupus familiaris
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Entity ID: 50
MoleculeChains LengthOrganismImage
RNA helicesXA [auth BX]113Canis lupus familiaris
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Entity ID: 51
MoleculeChains LengthOrganismImage
5S Ribosomal RNAYA [auth BY]115Canis lupus familiaris
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Entity ID: 52
MoleculeChains LengthOrganismImage
E site t-RNAZA [auth BZ]72Canis lupus familiaris
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2015-03-25
    Changes: Other
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Refinement description