5MMI

Structure of the large subunit of the chloroplast ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The complete structure of the chloroplast 70S ribosome in complex with translation factor pY.

Bieri, P.Leibundgut, M.Saurer, M.Boehringer, D.Ban, N.

(2017) EMBO J 36: 475-486

  • DOI: 10.15252/embj.201695959
  • Primary Citation of Related Structures:  
    5MMI, 5MMJ, 5MMM

  • PubMed Abstract: 
  • Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis ...

    Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo-EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid-specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid-specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light- and temperature-dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A-site and P-site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non-rotated state, in which the intersubunit bridges to the large subunit are stabilized.


    Organizational Affiliation

    Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland ban@mol.biol.ethz.ch.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31A [auth 0]130Spinacia oleraceaMutation(s): 0 
Gene Names: RPL31SOVF_125040
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32, chloroplasticB [auth 1]57Spinacia oleraceaMutation(s): 0 
Gene Names: rpl32
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L33, chloroplasticC [auth 2]66Spinacia oleraceaMutation(s): 0 
Gene Names: rpl33
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34, chloroplasticD [auth 3]152Spinacia oleraceaMutation(s): 0 
Gene Names: RPL34SOVF_073030
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35, chloroplasticE [auth 4]159Spinacia oleraceaMutation(s): 0 
Gene Names: RPL35SOVF_080710
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L36, chloroplasticF [auth 5]37Spinacia oleraceaMutation(s): 0 
Gene Names: rpl36
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein cL37, PSRP5G [auth 6]142Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP5RPL40SOVF_000530
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein 6, chloroplasticH [auth 7]116Spinacia oleraceaMutation(s): 0 
Gene Names: PSRP6SOVF_082300
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2, chloroplasticK [auth C]272Spinacia oleraceaMutation(s): 0 
Gene Names: rpl2-Arpl2-B
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL3cL [auth D]305Spinacia oleraceaMutation(s): 0 
Gene Names: RPL3SOVF_195350
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL4cM [auth E]293Spinacia oleraceaMutation(s): 0 
Gene Names: RPL4SOVF_029280
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL5cN [auth F]258Spinacia oleraceaMutation(s): 0 
Gene Names: RPL5PrpL5SOVF_057730
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL6cO [auth G]220Spinacia oleraceaMutation(s): 0 
Gene Names: RPL6SOVF_107200
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Entity ID: 16
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plastid ribosomal protein bL9cP [auth H]196Spinacia oleraceaMutation(s): 0 
Gene Names: RPL9SOVF_040960
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL10cQ [auth I]232Spinacia oleraceaMutation(s): 0 
Gene Names: RPL10SOVF_110360
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L11, chloroplasticR [auth J]224Spinacia oleraceaMutation(s): 0 
Gene Names: rpl11SOVF_048900
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Entity ID: 19
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50S ribosomal protein L13, chloroplasticS [auth K]250Spinacia oleraceaMutation(s): 0 
Gene Names: RPL13SOVF_093170
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Entity ID: 20
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50S ribosomal protein L14, chloroplasticT [auth L]121Spinacia oleraceaMutation(s): 0 
Gene Names: rpl14
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL15cU [auth M]271Spinacia oleraceaMutation(s): 0 
Gene Names: RPL15SOVF_177460
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Entity ID: 22
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50S ribosomal protein L16, chloroplasticV [auth N]135Spinacia oleraceaMutation(s): 0 
Gene Names: rpl16
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein bL17cW [auth O]126Spinacia oleraceaMutation(s): 0 
Gene Names: RPL17SOVF_059230
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL18cX [auth P]166Spinacia oleraceaMutation(s): 0 
Gene Names: RPL18PRPL18SOVF_159210
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19, chloroplasticY [auth Q]233Spinacia oleraceaMutation(s): 0 
Gene Names: RPL19PRPL19SOVF_150800
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20, chloroplasticZ [auth R]128Spinacia oleraceaMutation(s): 0 
Gene Names: rpl20
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21, chloroplasticAA [auth S]256Spinacia oleraceaMutation(s): 0 
Gene Names: RPL21SOVF_056040
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22, chloroplasticBA [auth T]199Spinacia oleraceaMutation(s): 0 
Gene Names: rpl22
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23, chloroplasticCA [auth U]198Spinacia oleraceaMutation(s): 0 
Gene Names: RPL23SOVF_109700
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL24cDA [auth V]192Spinacia oleraceaMutation(s): 0 
Gene Names: RPL24SOVF_183870
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein bL27cFA [auth X]194Spinacia oleraceaMutation(s): 0 
Gene Names: RPL27SOVF_107450
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein bL28cGA [auth Y]148Spinacia oleraceaMutation(s): 0 
Gene Names: RPL28SOVF_085320
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
plastid ribosomal protein uL29cHA [auth Z]168Spinacia oleraceaMutation(s): 0 
Gene Names: RPL29SOVF_096810
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Entity ID: 9
MoleculeChainsLengthOrganismImage
23S ribosomal RNAI [auth A]2,810Spinacia oleracea
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Entity ID: 10
MoleculeChainsLengthOrganismImage
5S ribosomal RNAJ [auth B]121Spinacia oleracea
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Entity ID: 31
MoleculeChainsLengthOrganismImage
4.5S ribosomal RNAEA [auth W]106Spinacia oleracea
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Entity ID: 35
MoleculeChainsLengthOrganismImage
E-site tRNAIA [auth z]2Spinacia oleracea
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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JA [auth 2],
LA [auth 5]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth A],
AJ [auth A],
AK [auth A],
AL [auth A],
AM [auth A],
AN [auth A],
AO [auth A],
AP [auth A],
AQ [auth A],
AR [auth A],
AS [auth B],
AT [auth V],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth A],
BM [auth A],
BN [auth A],
BO [auth A],
BP [auth A],
BQ [auth A],
BR [auth A],
BS [auth B],
BT [auth V],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth A],
CJ [auth A],
CK [auth A],
CL [auth A],
CM [auth A],
CN [auth A],
CO [auth A],
CP [auth A],
CQ [auth A],
CR [auth A],
CS [auth B],
CT [auth W],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
DF [auth A],
DG [auth A],
DH [auth A],
DI [auth A],
DJ [auth A],
DK [auth A],
DL [auth A],
DM [auth A],
DN [auth A],
DO [auth A],
DP [auth A],
DQ [auth A],
DR [auth A],
DS [auth B],
DT [auth W],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
EF [auth A],
EG [auth A],
EH [auth A],
EI [auth A],
EJ [auth A],
EK [auth A],
EL [auth A],
EM [auth A],
EN [auth A],
EO [auth A],
EP [auth A],
EQ [auth A],
ER [auth A],
ES [auth B],
ET [auth W],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
FI [auth A],
FJ [auth A],
FK [auth A],
FL [auth A],
FM [auth A],
FN [auth A],
FO [auth A],
FP [auth A],
FQ [auth A],
FR [auth A],
FS [auth B],
FT [auth W],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
GI [auth A],
GJ [auth A],
GK [auth A],
GL [auth A],
GM [auth A],
GN [auth A],
GO [auth A],
GP [auth A],
GQ [auth A],
GR [auth A],
GS [auth B],
GT [auth W],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
HI [auth A],
HJ [auth A],
HK [auth A],
HL [auth A],
HM [auth A],
HN [auth A],
HO [auth A],
HP [auth A],
HQ [auth A],
HR [auth A],
HS [auth B],
HT [auth W],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
IF [auth A],
IG [auth A],
IH [auth A],
II [auth A],
IJ [auth A],
IK [auth A],
IL [auth A],
IM [auth A],
IN [auth A],
IO [auth A],
IP [auth A],
IQ [auth A],
IR [auth A],
IS [auth B],
IT [auth W],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth A],
JI [auth A],
JJ [auth A],
JK [auth A],
JL [auth A],
JM [auth A],
JN [auth A],
JO [auth A],
JP [auth A],
JQ [auth A],
JR [auth A],
JS [auth B],
JT [auth W],
KA [auth 4],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
KF [auth A],
KG [auth A],
KH [auth A],
KI [auth A],
KJ [auth A],
KK [auth A],
KL [auth A],
KM [auth A],
KN [auth A],
KO [auth A],
KP [auth A],
KQ [auth A],
KR [auth A],
KS [auth B],
KT [auth W],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
LF [auth A],
LG [auth A],
LH [auth A],
LI [auth A],
LJ [auth A],
LK [auth A],
LL [auth A],
LM [auth A],
LN [auth A],
LO [auth A],
LP [auth A],
LQ [auth A],
LR [auth A],
LS [auth B],
LT [auth W],
MA [auth 6],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth A],
MG [auth A],
MH [auth A],
MI [auth A],
MJ [auth A],
MK [auth A],
ML [auth A],
MM [auth A],
MN [auth A],
MO [auth A],
MP [auth A],
MQ [auth A],
MR [auth A],
MS [auth B],
MT [auth W],
NA [auth 7],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
NH [auth A],
NI [auth A],
NJ [auth A],
NK [auth A],
NL [auth A],
NM [auth A],
NN [auth A],
NO [auth A],
NP [auth A],
NQ [auth A],
NR [auth A],
NS [auth B],
NT [auth W],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
OH [auth A],
OI [auth A],
OJ [auth A],
OK [auth A],
OL [auth A],
OM [auth A],
ON [auth A],
OO [auth A],
OP [auth A],
OQ [auth A],
OR [auth A],
OS [auth C],
OT [auth W],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PH [auth A],
PI [auth A],
PJ [auth A],
PK [auth A],
PL [auth A],
PM [auth A],
PN [auth A],
PO [auth A],
PP [auth A],
PQ [auth A],
PR [auth A],
PS [auth D],
PT [auth W],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth A],
QF [auth A],
QG [auth A],
QH [auth A],
QI [auth A],
QJ [auth A],
QK [auth A],
QL [auth A],
QM [auth A],
QN [auth A],
QO [auth A],
QP [auth A],
QQ [auth A],
QR [auth A],
QS [auth D],
QT [auth X],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RH [auth A],
RI [auth A],
RJ [auth A],
RK [auth A],
RL [auth A],
RM [auth A],
RN [auth A],
RO [auth A],
RP [auth A],
RQ [auth A],
RR [auth A],
RS [auth E],
RT [auth Y],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth A],
SG [auth A],
SH [auth A],
SI [auth A],
SJ [auth A],
SK [auth A],
SL [auth A],
SM [auth A],
SN [auth A],
SO [auth A],
SP [auth A],
SQ [auth A],
SR [auth A],
SS [auth H],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth A],
TF [auth A],
TG [auth A],
TH [auth A],
TI [auth A],
TJ [auth A],
TK [auth A],
TL [auth A],
TM [auth A],
TN [auth A],
TO [auth A],
TP [auth A],
TQ [auth A],
TR [auth A],
TS [auth M],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth A],
UL [auth A],
UM [auth A],
UN [auth A],
UO [auth A],
UP [auth A],
UQ [auth A],
UR [auth A],
US [auth M],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth A],
VI [auth A],
VJ [auth A],
VK [auth A],
VL [auth A],
VM [auth A],
VN [auth A],
VO [auth A],
VP [auth A],
VQ [auth A],
VR [auth A],
VS [auth N],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth A],
WI [auth A],
WJ [auth A],
WK [auth A],
WL [auth A],
WM [auth A],
WN [auth A],
WO [auth A],
WP [auth A],
WQ [auth A],
WR [auth A],
WS [auth P],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XE [auth A],
XF [auth A],
XG [auth A],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth A],
XL [auth A],
XM [auth A],
XN [auth A],
XO [auth A],
XP [auth A],
XQ [auth A],
XR [auth A],
XS [auth R],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth A],
YL [auth A],
YM [auth A],
YN [auth A],
YO [auth A],
YP [auth A],
YQ [auth A],
YR [auth A],
YS [auth T],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZE [auth A],
ZF [auth A],
ZG [auth A],
ZH [auth A],
ZI [auth A],
ZJ [auth A],
ZK [auth A],
ZL [auth A],
ZM [auth A],
ZN [auth A],
ZO [auth A],
ZP [auth A],
ZQ [auth A],
ZR [auth B],
ZS [auth U]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTPHENIX1.11.1

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Data collection, Derived calculations
  • Version 1.3: 2018-10-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-12-11
    Changes: Other