5MYJ

Structure of 70S ribosome from Lactococcus lactis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy.

Franken, L.E.Oostergetel, G.T.Pijning, T.Puri, P.Arkhipova, V.Boekema, E.J.Poolman, B.Guskov, A.

(2017) Nat Commun 8: 722-722

  • DOI: 10.1038/s41467-017-00718-x
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we re ...

    Bacteria downregulate their ribosomal activity through dimerization of 70S ribosomes, yielding inactive 100S complexes. In Escherichia coli, dimerization is mediated by the hibernation promotion factor (HPF) and ribosome modulation factor. Here we report the cryo-electron microscopy study on 100S ribosomes from Lactococcus lactis and a dimerization mechanism involving a single protein: HPF long . The N-terminal domain of HPF long binds at the same site as HPF in Escherichia coli 100S ribosomes. Contrary to ribosome modulation factor, the C-terminal domain of HPF long binds exactly at the dimer interface. Furthermore, ribosomes from Lactococcus lactis do not undergo conformational changes in the 30S head domains upon binding of HPF long , and the Shine-Dalgarno sequence and mRNA entrance tunnel remain accessible. Ribosome activity is blocked by HPF long due to the inhibition of mRNA recognition by the platform binding center. Phylogenetic analysis of HPF proteins suggests that HPF long -mediated dimerization is a widespread mechanism of ribosome hibernation in bacteria.When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.


    Organizational Affiliation

    Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. a.guskov@rug.nl.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB
255Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsBllmg_2430
Find proteins for A2RNV0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNV0

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC
217Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsCllmg_2377
Find proteins for A2RNP9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD
203Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsDllmg_0296
Find proteins for A2RI10 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE
168Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsEllmg_2364
Find proteins for A2RNN6 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF
97Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsFllmg_2475
Find proteins for A2RNZ4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG
155Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsGllmg_2557
Find proteins for A2RP73 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH
132Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsHllmg_2367
Find proteins for A2RNN9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI
130Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsIllmg_2545
Find proteins for A2RP61 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ
102Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsJllmg_2384
Find proteins for A2RNQ6 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK
127Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsKllmg_2355
Find proteins for A2RNM8 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL
137Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsLllmg_2558
Find proteins for A2RP74 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM
121Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsMllmg_2356
Find proteins for A2RNM9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
AN
61Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsZrpsNllmg_2370
Find proteins for A2RNP2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO
89Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsOllmg_2078
Find proteins for A2RMV9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP
90Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsPllmg_0932
Find proteins for A2RJS1 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RJS1

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ
86Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsQllmg_2374
Find proteins for A2RNP6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP6

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR
81Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsRllmg_2473
Find proteins for A2RNZ2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNZ2

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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS
92Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsSllmg_2379
Find proteins for A2RNQ1 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT
77Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsTllmg_1921
Find proteins for A2RMG0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S21
AU
58Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpsUllmg_0251
Find proteins for A2RHW9 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
B0
64Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmBllmg_0204
Find proteins for A2RHS3 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
B1
69Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmCllmg_2375
Find proteins for A2RNP7 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
B2
59Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmDllmg_2363
Find proteins for A2RNN5 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31 type B
B3
81Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmE2llmg_0906
Find proteins for A2RJP7 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B4
57Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmFllmg_0099
Find proteins for A2RHH0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RHH0

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33 3
B5
49Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmG3rpmGCllmg_2390
Find proteins for A2RNR2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNR2

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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B6
44Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmHllmg_0145
Find proteins for A2RHL6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RHL6

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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B7
66Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmIllmg_2030
Find proteins for A2RMR2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B8
38Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmJllmg_2357
Find proteins for A2RNN0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN0

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD
276Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplBllmg_2380
Find proteins for A2RNQ2 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ2

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE
207Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplCllmg_2383
Find proteins for A2RNQ5 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF
208Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplDllmg_2382
Find proteins for A2RNQ4 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNQ4

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG
180Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplEllmg_2371
Find proteins for A2RNP3 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNP3

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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH
178Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplFllmg_2366
Find proteins for A2RNN8 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNN8

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BM
148Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplMllmg_2546
Find proteins for A2RP62 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RP62

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BN
122Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplNllmg_2373
Find proteins for A2RNP5 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BO
147Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplOllmg_2362
Find proteins for A2RNN4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BP
137Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplPllmg_2376
Find proteins for A2RNP8 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BQ
126Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplQllmg_2353
Find proteins for A2RNM6 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RNM6

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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BR
115Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplRllmg_2365
Find proteins for A2RNN7 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BS
114Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplSllmg_1671
Find proteins for A2RLS5 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BT
119Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplTllmg_2029
Find proteins for A2RMR1 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BU
104Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplUllmg_1493
Find proteins for A2RLA4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BV
115Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplVllmg_2378
Find proteins for A2RNQ0 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BW
97Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplWllmg_2381
Find proteins for A2RNQ3 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BX
101Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rplXllmg_2372
Find proteins for A2RNP4 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BZ
94Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: rpmAllmg_1491
Find proteins for A2RLA2 (Lactococcus lactis subsp. cremoris (strain MG1363))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
Ribosome hibernation promotion factor
A
185Lactococcus lactis subsp. cremoris MG1363Mutation(s): 0 
Gene Names: hpfyfiAllmg_0616
Find proteins for A2RIX0 (Lactococcus lactis subsp. cremoris (strain MG1363))
Go to UniProtKB:  A2RIX0

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Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA1535Lactococcus lactis subsp. cremoris MG1363

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Entity ID: 31
MoleculeChainsLengthOrganism
23S ribosomal RNABA2897Lactococcus lactis subsp. cremoris MG1363

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Entity ID: 32
MoleculeChainsLengthOrganism
5S ribosomal RNABB115Lactococcus lactis subsp. cremoris MG1363
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NWONetherlandsTOPGO L.10.060
European Research CouncilNetherlandsERC-2014-ADG

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release