4V3P

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 34.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report


This is version 1.8 of the entry. See complete history


Literature

The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

Myasnikov, A.G.Afonina, Z.A.Menetret, J.F.Shirokov, V.A.Spirin, A.S.Klaholz, B.P.

(2014) Nat Commun 5: 5294-5294

  • DOI: 10.1038/ncomms6294
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from ...

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.


    Organizational Affiliation

    1] Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France [2] Centre National de la Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France [3] Institut National de la Santé et de la Recherche Médicale (INSERM), 67404 Illkirch, France [4] Université de Strasbourg, 67400 Strasbourg, France.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
G protein beta subunitSa380Triticum aestivumMutation(s): 0 
Gene Names: TaGB1
Find proteins for Q8LNY6 (Triticum aestivum)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Putative 40S ribosomal protein S3SB208Triticum aestivumMutation(s): 0 
Find proteins for Q8L804 (Triticum aestivum)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4SD200Triticum aestivumMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2SE263Triticum aestivumMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5SF191Triticum aestivumMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20SJ128Triticum aestivumMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18SM152Triticum aestivumMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13-1SO121Triticum aestivumMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-4SQ141Triticum aestivumMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30SZ62Triticum aestivumMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 3Sb36Triticum aestivumMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein S15SH130Triticum aestivumMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21ST82Triticum aestivumMutation(s): 0 
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
Ribosomal proteinLA216Triticum aestivumMutation(s): 0 
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7aLH201Triticum aestivumMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
Ribosomal Pr 117LM140Triticum aestivumMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L15LP194Triticum aestivumMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21LU164Triticum aestivumMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17LV171Triticum aestivumMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23aLX122Triticum aestivumMutation(s): 0 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24LZ75Triticum aestivumMutation(s): 0 
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein l28Lb73Triticum aestivumMutation(s): 0 
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30Lf112Triticum aestivumMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31Lg120Triticum aestivumMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
Ribosomal L32Lh133Triticum aestivumMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L37Ll94Triticum aestivumMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 3Lz14Triticum aestivumMutation(s): 0 
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6LG219Triticum aestivumMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18aLS167Triticum aestivumMutation(s): 0 
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22LW108Triticum aestivumMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27La99Triticum aestivumMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36Lk77Triticum aestivumMutation(s): 0 
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40-1Lp41Triticum aestivumMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0Ls262Triticum aestivumMutation(s): 0 
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L3LC389Triticum aestivumMutation(s): 0 
Gene Names: RPL3RPL3-A1RPL3A-1
Find proteins for Q7X744 (Triticum aestivum)
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4/L1LD372Triticum aestivumMutation(s): 0 
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L13aLK206Triticum aestivumMutation(s): 0 
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37a, expressedLm92Triticum aestivumMutation(s): 0 
Gene Names: TAA_ctg0616b.00240.1TRAES_3BF073800030CFD_c1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23SL142Triticum aestivumMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11SP85Triticum aestivumMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19SS146Triticum aestivumMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15SR91Triticum aestivumMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25SV100Triticum aestivumMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S WHEAT GERM RIBOSOME1SW92Triticum aestivumMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28SY58Triticum aestivumMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein SASA260Triticum aestivumMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 2Sc25Triticum aestivumMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 3SU98Triticum aestivumMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27SX50Triticum aestivumMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9SC195Triticum aestivumMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
Unknown 40S wheat germ ribosome protein 4SG143Triticum aestivumMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29SN48Triticum aestivumMutation(s): 0 
Gene Names: RPS29
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2LB255Triticum aestivumMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L11LE170Triticum aestivumMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9LF190Triticum aestivumMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27a-3LO144Triticum aestivumMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18LR163Triticum aestivumMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5LQ304Triticum aestivumMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L19LT189Triticum aestivumMutation(s): 1 
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26LY130Triticum aestivumMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29Ld23Triticum aestivumMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38Ln69Triticum aestivumMutation(s): 0 
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L39Lo51Triticum aestivumMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L44Lr105Triticum aestivumMutation(s): 0 
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 1Lq25Triticum aestivumMutation(s): 0 
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 2Lx, Ly20Triticum aestivumMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 5LL182Triticum aestivumMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
Unknown 60S wheat germ ribosome protein 6LN134Triticum aestivumMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16SI126Triticum aestivumMutation(s): 0 
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein l34Li119Triticum aestivumMutation(s): 0 
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein L35ALj104Triticum aestivumMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12LJ128Triticum aestivumMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein P1Lt, Lu58Triticum aestivumMutation(s): 0 
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P2ALv, Lw59Triticum aestivumMutation(s): 0 
Gene Names: CAMPLR22A2D_LOCUS2926
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35Lc124Triticum aestivumMutation(s): 0 
Gene Names: RPL35
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
Ribosomal protein L7Le244Triticum aestivumMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10-1LI184Triticum aestivumMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14SK119Triticum aestivumMutation(s): 0 
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Entity ID: 30
MoleculeChainsLengthOrganism
40S WHEAT GERM RIBOSOME protein 4S311Triticum aestivum

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Entity ID: 33
MoleculeChainsLengthOrganism
26S ribosomal RNAL13352Triticum aestivum

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Entity ID: 35
MoleculeChainsLengthOrganism
5.8S ribosomal RNAL2159Triticum aestivum

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Entity ID: 31
MoleculeChainsLengthOrganism
40S ribosomal RNAS275Triticum aestivum

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Entity ID: 32
MoleculeChainsLengthOrganism
18S ribosomal RNAS11743Triticum aestivum

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Entity ID: 34
MoleculeChainsLengthOrganism
5S ribosomal RNAL3120Triticum aestivum
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 34.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-22
    Type: Initial release
  • Version 1.1: 2016-12-14
    Changes: Atomic model
  • Version 1.2: 2017-06-28
    Changes: Data collection, Refinement description, Structure summary
  • Version 1.3: 2017-07-26
    Changes: Database references, Structure summary
  • Version 1.4: 2017-08-23
    Changes: Data collection, Derived calculations
  • Version 1.5: 2018-06-20
    Changes: Advisory, Data collection, Database references, Derived calculations
  • Version 1.6: 2018-10-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.7: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.8: 2019-12-18
    Changes: Other