6XDR

Escherichia coli transcription-translation complex B (TTC-B) containing an 27 nt long mRNA spacer, NusG, and fMet-tRNAs at E-site and P-site


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of transcription-translation coupling.

Wang, C.Molodtsov, V.Firlar, E.Kaelber, J.T.Blaha, G.Su, M.Ebright, R.H.

(2020) Science 369: 1359-1365

  • DOI: 10.1126/science.abb5317
  • Primary Citation of Related Structures:  
    6VU3, 6VYQ, 6VYR, 6VYS, 6VYT, 6VYU, 6VYW, 6VYX, 6VYY, 6VYZ, 6VZ2, 6VZ3, 6VZ5, 6VZ7, 6VZJ, 6X6T, 6X7F, 6X7K, 6X9Q, 6XDQ, 6XDR, 6XGF, 6XII, 6XIJ

  • PubMed Abstract: 
  • In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA ...

    In bacteria, transcription and translation are coupled processes in which the movement of RNA polymerase (RNAP)-synthesizing messenger RNA (mRNA) is coordinated with the movement of the first ribosome-translating mRNA. Coupling is modulated by the transcription factors NusG (which is thought to bridge RNAP and the ribosome) and NusA. Here, we report cryo-electron microscopy structures of Escherichia coli transcription-translation complexes (TTCs) containing different-length mRNA spacers between RNAP and the ribosome active-center P site. Structures of TTCs containing short spacers show a state incompatible with NusG bridging and NusA binding (TTC-A, previously termed "expressome"). Structures of TTCs containing longer spacers reveal a new state compatible with NusG bridging and NusA binding (TTC-B) and reveal how NusG bridges and NusA binds. We propose that TTC-B mediates NusG- and NusA-dependent transcription-translation coupling.


    Organizational Affiliation

    Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA. minsu@umich.edu ebright@waksman.rutgers.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21A [auth 0]103Escherichia coliMutation(s): 0 
Gene Names: rplU
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22B [auth 1]110Escherichia coliMutation(s): 0 
Gene Names: rplV
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23C [auth 2]100Escherichia coliMutation(s): 0 
Gene Names: rplW
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24D [auth 3]104Escherichia coliMutation(s): 0 
Gene Names: rplX
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25E [auth 4]94Escherichia coliMutation(s): 0 
Gene Names: rplY
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Find proteins for D7XH79 (Escherichia coli MS 84-1)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L10I [auth 9]165Escherichia coliMutation(s): 0 
Gene Names: rplJ
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaK [auth AA]1,342Escherichia coliMutation(s): 0 
Gene Names: rpoBZ5560ECs4910
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription termination/antitermination protein NusGL [auth AB]181Escherichia coliMutation(s): 0 
Gene Names: nusGV415_18420
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaM [auth AC],
N [auth AD]
329Escherichia coliMutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'O [auth AE]1,407Escherichia coliMutation(s): 1 
Gene Names: rpoCBvCmsKKP036_03580EYX47_21890
EC: 2.7.7.6
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Find proteins for A0A4S1NBU2 (Escherichia coli)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaP [auth AF]91Escherichia coliMutation(s): 0 
Gene Names: rpoZZ5075ECs4524
EC: 2.7.7.6
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Entity ID: 16
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30S ribosomal protein S18R [auth C]75Escherichia coliMutation(s): 0 
Gene Names: rpsR
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth E]87Escherichia coliMutation(s): 0 
Gene Names: rpsT
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21U [auth F]71Escherichia coliMutation(s): 0 
Gene Names: rpsU
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Entity ID: 20
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30S ribosomal protein S2V [auth G]241Escherichia coliMutation(s): 0 
Gene Names: rpsB
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Entity ID: 21
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30S ribosomal protein S1W [auth H]557Escherichia coliMutation(s): 0 
Gene Names: ECCG_01333
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Entity ID: 22
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30S ribosomal protein S3X [auth I]233Escherichia coliMutation(s): 0 
Gene Names: rpsC
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S4Y [auth J]206Escherichia coliMutation(s): 0 
Gene Names: rpsD
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S5Z [auth K]167Escherichia coliMutation(s): 0 
Gene Names: rpsE
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S6AA [auth L]135Escherichia coliMutation(s): 0 
Gene Names: rpsFb4200JW4158
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S7BA [auth M]179Escherichia coliMutation(s): 0 
Gene Names: rpsGGHR40_06850
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S8CA [auth N]130Escherichia coliMutation(s): 0 
Gene Names: rpsH
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S9DA [auth O]130Escherichia coliMutation(s): 0 
Gene Names: rpsI
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Entity ID: 29
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30S ribosomal protein S10EA [auth P]103Escherichia coliMutation(s): 0 
Gene Names: rpsJ
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Entity ID: 30
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30S ribosomal protein S11FA [auth Q]129Escherichia coliMutation(s): 0 
Gene Names: rpsK
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S12GA [auth R]124Escherichia coliMutation(s): 0 
Gene Names: rpsL
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S14HA [auth S]101Escherichia coliMutation(s): 0 
Gene Names: rpsN
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S15IA [auth T]89Escherichia coliMutation(s): 0 
Gene Names: rpsO
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16JA [auth U]82Escherichia coliMutation(s): 0 
Gene Names: rpsP
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S17KA [auth V]84Escherichia coliMutation(s): 0 
Gene Names: rpsQ
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S19LA [auth W]92Escherichia coliMutation(s): 0 
Gene Names: rpsS
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Entity ID: 37
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30S ribosomal protein S13MA [auth X]118Escherichia coliMutation(s): 0 
Gene Names: rpsM
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Entity ID: 38
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50S ribosomal protein L11NA [auth Y]142Escherichia coliMutation(s): 0 
Gene Names: rplK
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L7/L12OA [auth Z]121Escherichia coliMutation(s): 0 
Gene Names: rplLECDEC2C_4837
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Entity ID: 41
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50S ribosomal protein L27QA [auth b]85Escherichia coliMutation(s): 0 
Gene Names: rpmAb3185JW3152
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Entity ID: 42
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50S ribosomal protein L28RA [auth c]78Escherichia coliMutation(s): 0 
Gene Names: rpmB
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Entity ID: 44
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50S ribosomal protein L29TA [auth e]63Escherichia coliMutation(s): 0 
Gene Names: rpmC
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Entity ID: 45
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50S ribosomal protein L30UA [auth f]59Escherichia coliMutation(s): 0 
Gene Names: rpmD
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Entity ID: 46
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50S ribosomal protein L31VA [auth g]70Escherichia coliMutation(s): 0 
Gene Names: rpmE
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Entity ID: 47
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50S ribosomal protein L2WA [auth h]273Escherichia coliMutation(s): 0 
Gene Names: rplBb3317JW3279
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Entity ID: 48
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50S ribosomal protein L32XA [auth i]57Escherichia coliMutation(s): 0 
Gene Names: rpmF
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Entity ID: 49
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50S ribosomal protein L3YA [auth j]209Escherichia coliMutation(s): 0 
Gene Names: rplCb3320JW3282
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Entity ID: 50
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50S ribosomal protein L33ZA [auth k]55Escherichia coliMutation(s): 0 
Gene Names: rpmG
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Entity ID: 51
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50S ribosomal protein L4AB [auth l]201Escherichia coliMutation(s): 0 
Gene Names: rplD
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Entity ID: 52
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50S ribosomal protein L34BB [auth m]46Escherichia coliMutation(s): 0 
Gene Names: rpmH
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Entity ID: 53
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50S ribosomal protein L5CB [auth n]179Escherichia coliMutation(s): 0 
Gene Names: rplE
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Entity ID: 54
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50S ribosomal protein L35DB [auth o]65Escherichia coliMutation(s): 0 
Gene Names: rpmI
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Entity ID: 55
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50S ribosomal protein L6EB [auth p]177Escherichia coliMutation(s): 0 
Gene Names: rplF
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Entity ID: 56
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50S ribosomal protein L36FB [auth q]38Escherichia coliMutation(s): 0 
Gene Names: rpmJ
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Entity ID: 57
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50S ribosomal protein L9GB [auth r]149Escherichia coliMutation(s): 0 
Gene Names: rplI
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Entity ID: 58
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50S ribosomal protein L13HB [auth s]142Escherichia coliMutation(s): 0 
Gene Names: rplM
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14IB [auth t]123Escherichia coliMutation(s): 0 
Gene Names: rplN
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Entity ID: 60
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50S ribosomal protein L15JB [auth u]144Escherichia coliMutation(s): 0 
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Find proteins for A0A037Y8L6 (Escherichia coli)
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Entity ID: 61
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50S ribosomal protein L16KB [auth v]136Escherichia coliMutation(s): 0 
Gene Names: rplPb3313JW3275
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Find proteins for P0ADY7 (Escherichia coli (strain K12))
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Entity ID: 62
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50S ribosomal protein L17LB [auth w]127Escherichia coliMutation(s): 0 
Gene Names: rplQECCG_03701
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18MB [auth x]117Escherichia coliMutation(s): 0 
Gene Names: rplR
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19NB [auth y]115Escherichia coliMutation(s): 0 
Gene Names: rplS
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20OB [auth z]118Escherichia coliMutation(s): 0 
Gene Names: rplT
UniProt
Find proteins for B7MAS6 (Escherichia coli O45:K1 (strain S88 / ExPEC))
Explore B7MAS6 
Go to UniProtKB:  B7MAS6
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UniProt GroupB7MAS6
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Entity ID: 6
MoleculeChainsLengthOrganismImage
NT DNAF [auth 5]36synthetic construct
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Entity ID: 7
MoleculeChainsLengthOrganismImage
T DNAG [auth 6]36synthetic construct
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Entity ID: 8
MoleculeChainsLengthOrganismImage
mRNA with 27 nt long spacerH [auth 7]44synthetic construct
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Entity ID: 10
MoleculeChainsLengthOrganismImage
E-site and P-site tRNA (fMet)J [auth A],
Q [auth B]
76Escherichia coli
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Entity ID: 17
MoleculeChainsLengthOrganismImage
16S rRNAS [auth D]1,542Escherichia coli
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Entity ID: 40
MoleculeChainsLengthOrganismImage
23S rRNAPA [auth a]2,904Escherichia coli
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Entity ID: 43
MoleculeChainsLengthOrganismImage
5S rRNASA [auth d]120Escherichia coli
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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QB [auth AE],
RB [auth AE]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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PB [auth AE]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-02
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references