9L5V | pdb_00009l5v

cryo-EM structure of PSII-ACPII from Rhodomonas sp. NIES-2332


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural analysis of PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte alga Rhodomonas sp. NIES-2332.

Zhang, W.Yonehara, N.Ishii, M.Jiang, H.La Rocca, R.Tsai, P.C.Li, H.Kato, K.Akita, F.Shen, J.R.

(2025) Front Plant Sci 16: 1716939-1716939

  • DOI: https://doi.org/10.3389/fpls.2025.1716939
  • Primary Citation of Related Structures:  
    9KZ9, 9L0K, 9L5V

  • PubMed Abstract: 

    Light energy is converted to chemical energy by two photosystems (PSI and PSII) in complex with their light-harvesting complex proteins (LHCI and LHCII) in photosynthesis. Rhodomonas is a member of cryptophyte alga whose LHCs contain unique chlorophyll a/c proteins (ACPs) and phycobiliproteins. We purified PSI-ACPI and PSII-ACPII supercomplexes from a cryptophyte Rhodomonas sp. NIES-2332 and analyzed their structures at high resolutions of 2.08 Å and 2.17 Å, respectively, using cryo-electron microscopy. These structures are largely similar to those reported previously from two other species of cryptophytes, but exhibited some differences in both the pigment locations and subunit structures. A part of the antenna subunits of both photosystems is shifted compared with the previously reported structures from other species of cryptophytes, suggesting some differences in the energy transfer rates from the antenna to the PSI and PSII cores. Newly identified lipids are found to occupy the interfaces between the antennae and cores, which may be important for assembly and stabilization of the supercomplexes. Water molecules surrounding three iron-sulfur clusters of the PSI core are found in our high-resolution structure, some of which are conserved from cyanobacteria to higher plants but some are different. In addition, our structure of PSII-ACPII lacks the subunits of oxygen-evolving complex as well as the Mn 4 CaO 5 cluster, suggesting that the cells are in the S-growth phase, yet the PSI-ACPI structure showed the binding of PsaQ, suggesting that it is in an L-phase. These results suggest that the S-phase and L-phase can co-exist in the cryptophytic cells. The high-resolution structures of both PSI-ACPIs and PSII-ACPIIs solved in this study provide a more solid structural basis for elucidating the energy transfer and quenching mechanisms in this group of the organisms.


  • Organizational Affiliation
    • Advanced Research Field, Research Institute for Interdisciplinary Science, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Q [auth a]
374Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.10.3.9
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
R [auth b]
508Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
S [auth c]
486Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
T [auth d]
351Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.10.3.9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
U [auth e]
84Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
V [auth f]
42Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
W [auth h]
67Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
X [auth i]
38Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KI [auth K],
Y [auth k]
45Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJ [auth L],
Z [auth l]
38Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein MAA [auth m],
K [auth M]
118Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TBA [auth t],
L [auth T]
32Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein WCA [auth w],
M [auth W]
121Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinDA [auth x],
N [auth X]
39Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30EA [auth y],
O [auth Y]
34Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZFA [auth z],
P [auth Z]
62Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-1GA [auth 1],
HA [auth N]
234Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-2IA [auth 2],
OA [auth O]
215Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-3JA [auth 3],
PA [auth P]
182Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-4KA [auth 4],
QA [auth Q]
200Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-5LA [auth 5],
RA [auth R]
228Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
ACPII-6MA [auth 6],
SA [auth S]
174Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Psb-gama_linkerNA [auth G]292Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Psb-gama_linkerTA [auth g]292Rhodomonas sp. NIES-2332Mutation(s): 0 
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Small Molecules
Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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FG [auth h],
JD [auth H],
PF [auth c],
QC [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AD [auth D]
AF [auth c]
AI [auth 2]
AJ [auth 3]
AL [auth 6]
AD [auth D],
AF [auth c],
AI [auth 2],
AJ [auth 3],
AL [auth 6],
BC [auth C],
BD [auth D],
BF [auth c],
BI [auth 2],
BJ [auth 3],
BL [auth 6],
CC [auth C],
CE [auth b],
CF [auth c],
CI [auth 2],
CJ [auth 3],
CK [auth 5],
CN [auth Q],
DC [auth C],
DE [auth b],
DF [auth c],
DI [auth 2],
DJ [auth 3],
DK [auth 5],
DL [auth 6],
DM [auth P],
DN [auth Q],
EC [auth C],
EE [auth b],
EF [auth c],
EI [auth 2],
EK [auth 5],
EL [auth 6],
EM [auth P],
EO [auth S],
FC [auth C],
FE [auth b],
FF [auth c],
FH [auth N],
FI [auth 2],
FK [auth 5],
FM [auth P],
FO [auth S],
GB [auth B],
GC [auth C],
GE [auth b],
GF [auth c],
GH [auth N],
GI [auth 2],
GK [auth 5],
GM [auth P],
GO [auth S],
HB [auth B],
HC [auth C],
HE [auth b],
HF [auth c],
HH [auth N],
HI [auth 2],
HK [auth 5],
HO [auth S],
IB [auth B],
IC [auth C],
IE [auth b],
IF [auth c],
IH [auth N],
II [auth 2],
IJ [auth 4],
IK [auth 5],
IL [auth G],
IM [auth P],
IO [auth S],
JB [auth B],
JC [auth C],
JE [auth b],
JF [auth c],
JJ [auth 4],
JK [auth 5],
JL [auth G],
JM [auth P],
JO [auth S],
KB [auth B],
KC [auth C],
KE [auth b],
KF [auth c],
KH [auth N],
KI [auth 2],
KJ [auth 4],
KK [auth 5],
KM [auth P],
KO [auth S],
LB [auth B],
LC [auth C],
LE [auth b],
LF [auth c],
LG [auth 1],
LH [auth N],
LI [auth 2],
LJ [auth 4],
LL [auth O],
LM [auth P],
MB [auth B],
MC [auth C],
ME [auth b],
MG [auth 1],
MH [auth N],
MK [auth 5],
ML [auth O],
MM [auth P],
MN [auth R],
MO [auth S],
NB [auth B],
NC [auth C],
NE [auth b],
NG [auth 1],
NH [auth N],
NJ [auth 4],
NK [auth 5],
NL [auth O],
NM [auth P],
NN [auth R],
NO [auth S],
OB [auth B],
OE [auth b],
OG [auth 1],
OJ [auth 4],
OL [auth O],
ON [auth R],
PB [auth B],
PE [auth b],
PJ [auth 4],
PL [auth O],
PN [auth R],
QB [auth B],
QD [auth a],
QE [auth b],
QG [auth 1],
QJ [auth 4],
QL [auth O],
QN [auth R],
RB [auth B],
RD [auth a],
RE [auth b],
RG [auth 1],
RH [auth N],
RL [auth O],
RN [auth R],
RO [auth g],
SB [auth B],
SG [auth 1],
SH [auth N],
SI [auth 2],
SL [auth O],
SM [auth Q],
SN [auth R],
SO [auth g],
TB [auth B],
TD [auth a],
TG [auth 1],
TJ [auth 4],
TL [auth O],
TM [auth Q],
TN [auth R],
UB [auth B],
UF [auth d],
UJ [auth 4],
UM [auth Q],
UN [auth R],
VA [auth A],
VB [auth B],
VI [auth 3],
VK [auth 6],
VL [auth O],
WA [auth A],
WI [auth 3],
WK [auth 6],
WL [auth O],
WM [auth Q],
WN [auth R],
XC [auth D],
XF [auth d],
XG [auth 1],
XI [auth 3],
XK [auth 6],
XM [auth Q],
XN [auth R],
YA [auth A],
YF [auth d],
YG [auth 1],
YK [auth 6],
YM [auth Q],
ZE [auth c],
ZI [auth 3],
ZK [auth 6],
ZM [auth Q]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO (Subject of Investigation/LOI)
Query on PHO

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SD [auth a],
VF [auth d],
XA [auth A],
YC [auth D]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

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BB [auth A],
UC [auth D],
WD [auth a],
XE [auth c]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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AK [auth 4]
BE [auth a]
BG [auth d]
BM [auth O]
DG [auth d]
AK [auth 4],
BE [auth a],
BG [auth d],
BM [auth O],
DG [auth d],
ED [auth D],
FB [auth A],
GD [auth D],
IG [auth m],
JN [auth Q],
LD [auth M],
LN [auth R],
RF [auth c],
RI [auth 2],
SC [auth C],
SF [auth c],
TC [auth C],
UK [auth 5],
VE [auth b],
WF [auth d],
ZB [auth B],
ZC [auth D]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9 (Subject of Investigation/LOI)
Query on PL9

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AB [auth A],
CD [auth D],
VD [auth a],
ZF [auth d]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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AC [auth C]
AG [auth d]
DD [auth D]
DO [auth R]
EH [auth 1]
AC [auth C],
AG [auth d],
DD [auth D],
DO [auth R],
EH [auth 1],
HG [auth l],
KD [auth L],
KG [auth z],
KL [auth G],
OD [auth Z],
QF [auth c],
RC [auth C],
TK [auth 5],
UI [auth 2],
WC [auth D],
WE [auth b],
XD [auth a],
ZH [auth N]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

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EG [auth f],
HD [auth F]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KC2 (Subject of Investigation/LOI)
Query on KC2

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AN [auth Q]
BN [auth Q]
CL [auth 6]
HM [auth P]
JH [auth N]
AN [auth Q],
BN [auth Q],
CL [auth 6],
HM [auth P],
JH [auth N],
JI [auth 2],
LK [auth 5],
LO [auth S],
MJ [auth 4],
OH [auth N],
PG [auth 1],
PH [auth N],
QH [auth N],
RJ [auth 4],
SJ [auth 4],
UG [auth 1],
UL [auth O],
VG [auth 1],
VM [auth Q],
VN [auth R],
WG [auth 1],
YI [auth 3]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0 (Subject of Investigation/LOI)
Query on II0

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AH [auth 1]
AO [auth R]
BH [auth 1]
BK [auth 4]
CH [auth 1]
AH [auth 1],
AO [auth R],
BH [auth 1],
BK [auth 4],
CH [auth 1],
CM [auth O],
CO [auth R],
EJ [auth 3],
EN [auth Q],
FJ [auth 3],
FL [auth 6],
FN [auth Q],
GJ [auth 3],
GL [auth 6],
GN [auth Q],
HL [auth 6],
HN [auth Q],
KN [auth Q],
MI [auth 2],
NI [auth 2],
OI [auth 2],
OK [auth 5],
OM [auth P],
OO [auth S],
PI [auth 2],
PK [auth 5],
PM [auth P],
PO [auth S],
QK [auth 5],
QM [auth P],
TH [auth N],
TI [auth 2],
UH [auth N],
VH [auth N],
VJ [auth 4],
WH [auth N],
WJ [auth 4],
XJ [auth 4],
XL [auth O],
YH [auth N],
YJ [auth 4],
YL [auth O],
YN [auth R],
ZG [auth 1],
ZL [auth O],
ZN [auth R]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
C40 H52 O2
DVICWXUADSCSLL-DDEWRDOISA-N
IHT (Subject of Investigation/LOI)
Query on IHT

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AM [auth O]
BO [auth R]
DH [auth 1]
IN [auth Q]
QI [auth 2]
AM [auth O],
BO [auth R],
DH [auth 1],
IN [auth Q],
QI [auth 2],
RK [auth 5],
XH [auth N],
ZJ [auth 4]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O
UNJKJDIRJWIHLL-BQLQDKTLSA-N
WVN (Subject of Investigation/LOI)
Query on WVN

Download Ideal Coordinates CCD File 
CG [auth d]
FD [auth D]
GG [auth k]
HJ [auth 3]
ID [auth H]
CG [auth d],
FD [auth D],
GG [auth k],
HJ [auth 3],
ID [auth H],
JG [auth x],
MD [auth Y],
MF [auth c],
ND [auth Z],
NF [auth c],
OC [auth C],
OF [auth c],
PC [auth C],
QO [auth S],
RM [auth P],
SE [auth b],
SK [auth 5],
TE [auth b],
UD [auth a],
UE [auth b],
WB [auth B],
XB [auth B],
YB [auth B],
ZA [auth A]
1,3,3-trimethyl-2-[(1E,3E,5E,7E,9E,11E,13E,15E,17E)-3,7,12,16-tetramethyl-18-[(1R)-2,6,6-trimethylcyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]cyclohexene
C40 H56
ANVAOWXLWRTKGA-NTXLUARGSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
TF [auth d],
VC [auth D]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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PD [auth a],
UA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
MN
Query on MN

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AE [auth a],
DB [auth A],
EB [auth A],
ZD [auth a]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CB [auth A],
YD [auth a],
YE [auth c]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP22H04916

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2025-12-31
    Changes: Data collection, Database references