4V6W | pdb_00004v6w

Structure of the D. melanogaster 80S ribosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

Structures of the human and Drosophila 80S ribosome.

Anger, A.M., Armache, J.-P., Berninghausen, O., Habeck, M., Subklewe, M., Wilson, D.N., Beckmann, R.

(2013) Nature 497: 80-85

  • DOI: https://doi.org/10.1038/nature12104
  • Primary Citation of Related Structures:  
    4V6W, 4V6X

  • PubMed Abstract: 

    Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments.

    • Organizational Affiliation: 

    Gene Center, Department of Biochemistry and Center for integrated Protein Science Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Elongation factor 2A [auth Az]844Drosophila melanogasterMutation(s): 0 
EC: 3.6.5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein subunit beta-like proteinB [auth Ag]318Drosophila melanogasterMutation(s): 0 
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Find proteins for O18640 (Drosophila melanogaster)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S20C [auth AU]120Drosophila melanogasterMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S10aD [auth AK]163Drosophila melanogasterMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S14E [auth AO]151Drosophila melanogasterMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S23F [auth AX]143Drosophila melanogasterMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S12G [auth AM]139Drosophila melanogasterMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S18H [auth AS]152Drosophila melanogasterMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S29I [auth Ad]56Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S13J [auth AN]151Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S11K [auth AL]155Drosophila melanogasterMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S17L [auth AR]131Drosophila melanogasterMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S15, isoform AM [auth AP]148Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S19aN [auth AT]156Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3aO [auth AB]268Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein SAP [auth AA]313Drosophila melanogasterMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S21Q [auth AV]83Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S24R [auth AY]131Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S25S [auth AZ]117Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S26T [auth Aa]114Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S27U [auth Ab]84Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S28V [auth Ac]65Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S3W [auth AD]246Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S30, isoform AX [auth Ae]132Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S27aY [auth Af]80Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S9Z [auth AJ]195Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
40S ribosomal protein S4AA [auth AE]261Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S2BA [auth AC]267Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S6CA [auth AG]248Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S5aDA [auth AF]228Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S7EA [auth AH]194Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S15AaFA [auth AW]130Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S8GA [auth AI]208Drosophila melanogasterMutation(s): 0 
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40S ribosomal protein S16HA [auth AQ]148Drosophila melanogasterMutation(s): 0 
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Vig2, isoform BIA [auth Ah]121Drosophila melanogasterMutation(s): 0 
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60S ribosomal protein L10a-2LA [auth Cz]218Drosophila melanogasterMutation(s): 0 
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60S acidic ribosomal protein P0MA [auth Cq]223Drosophila melanogasterMutation(s): 0 
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GTEx:  ENSG00000089157 
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60S ribosomal protein L12NA [auth CK]165Drosophila melanogasterMutation(s): 0 
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60S ribosomal protein L13aOA [auth CO]205Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13PA [auth CL]218Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23QA [auth CV]140Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14RA [auth CM]166Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aSA [auth Ca]149Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15TA [auth CN]204Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10UA [auth CI]218Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5VA [auth CD]299Drosophila melanogasterMutation(s): 0 
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MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18WA [auth CQ]188Drosophila melanogasterMutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19XA [auth CR]203Drosophila melanogasterMutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8YA [auth CA]256Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aZA [auth CS]177Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21AB [auth CT]159Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17BB [auth CP]186Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22CB [auth CU]299Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23ADB [auth CX]277Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26EB [auth CY]149Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24FB [auth CW]155Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 59
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27GB [auth CZ]135Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 60
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28HB [auth Cr]144Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 61
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35IB [auth Ch]123Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 62
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29JB [auth Cb]76Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 63
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3KB [auth CB]416Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 64
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7LB [auth CF]252Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 65
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30MB [auth Cc]111Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 66
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31NB [auth Cd]124Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 67
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32OB [auth Ce]134Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 68
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35APB [auth Cf]157Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 69
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34aQB [auth Cg]162Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 70
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36RB [auth Ci]115Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 71
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-ASB [auth Cj]93Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 72
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38TB [auth Ck]70Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 73
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39UB [auth Cl]51Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 74
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4VB [auth CC]401Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 75
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40WB [auth Cm]52Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 76
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41XB [auth Cn]25Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 77
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aYB [auth Cp]92Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 78
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36AZB [auth Co]104Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 79
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11AC [auth CJ]184Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 80
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9BC [auth CH]190Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 81
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6, isoform ACC [auth CE]243Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 82
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aDC [auth CG]271Drosophila melanogasterMutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains LengthOrganismImage
18S ribosomal RNAJA [auth B2]1,995Drosophila melanogaster
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Entity ID: 37
MoleculeChains LengthOrganismImage
E-tRNAKA [auth BC]75Drosophila melanogaster
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Entity ID: 83
MoleculeChains LengthOrganismImage
28S ribosomal RNAEC [auth A5]3,970Drosophila melanogaster
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Entity ID: 84
MoleculeChains LengthOrganismImage
2S ribosomal RNAFC [auth A9]30Drosophila melanogaster
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Entity ID: 85
MoleculeChains LengthOrganismImage
5S ribosomal RNAGC [auth A7]120Drosophila melanogaster
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Entity ID: 86
MoleculeChains LengthOrganismImage
5.8S ribosomal RNAHC [auth A8]123Drosophila melanogaster
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONSPIDER

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: 2015-04-08
    Changes: Other
  • Version 1.3: 2018-07-18
    Changes: Data collection
  • Version 1.4: 2019-12-18
    Changes: Database references, Other
  • Version 1.5: 2023-02-01
    Changes: Database references
  • Version 1.6: 2024-05-15
    Changes: Data collection