9L0K | pdb_00009l0k

Cryo-EM structure of PSI-11ACPIs from Rhodomonas sp. NIES-2332 at 2.14 angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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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 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.

Macromolecule Content 

  • Total Structure Weight: 852.36 kDa 
  • Atom Count: 53,701 
  • Modeled Residue Count: 4,544 
  • Deposited Residue Count: 5,345 
  • Unique protein chains: 24

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1752Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.97.1.12
UniProt
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UniProt GroupO78508
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A6MVZ6 (Rhodomonas salina)
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UniProt GroupA6MVZ6
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A6MVS8 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II141Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV64Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MW36 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III188Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVU7 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]42Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVU6 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII [auth L]153Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVV8 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]30Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVT4 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK87Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVS9 (Rhodomonas salina)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-sL [auth s]302Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-cM [auth c]215Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-aN [auth a]217Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-bO [auth b]236Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-hP [auth h]229Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-mQ [auth m],
U [auth j]
212Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-lR [auth l]175Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-kS [auth k]232Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-iT [auth i]200Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-dV [auth d]219Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaRW [auth R]135Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPI-nX [auth n]220Rhodomonas sp. NIES-2332Mutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
PsaQY [auth Q]233Rhodomonas sp. NIES-2332Mutation(s): 0 

Small Molecules

Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
WD [auth B],
WL [auth j]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth A]
AB [auth A]
AD [auth B]
AG [auth c]
AI [auth h]
AA [auth A],
AB [auth A],
AD [auth B],
AG [auth c],
AI [auth h],
AK [auth k],
AM [auth d],
AN [auth n],
BA [auth A],
BB [auth A],
BD [auth B],
BM [auth d],
BN [auth n],
CA [auth A],
CB [auth A],
CC [auth A],
CD [auth B],
CH [auth b],
CJ [auth l],
CM [auth d],
CN [auth n],
DA [auth A],
DB [auth A],
DD [auth B],
DH [auth b],
DJ [auth l],
DM [auth d],
EA [auth A],
EB [auth A],
ED [auth B],
EF [auth K],
EH [auth b],
EJ [auth l],
EK [auth k],
EM [auth d],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FH [auth b],
FI [auth h],
FJ [auth l],
FL [auth j],
FM [auth d],
FN [auth n],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GH [auth b],
GI [auth m],
GJ [auth l],
GL [auth j],
GM [auth d],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth s],
HH [auth b],
HI [auth m],
HJ [auth l],
HL [auth j],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IE [auth F],
IF [auth s],
IH [auth b],
II [auth m],
IJ [auth l],
IL [auth j],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth F],
JG [auth a],
JH [auth b],
JI [auth m],
JJ [auth l],
JL [auth j],
JM [auth d],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KG [auth a],
KH [auth b],
KI [auth m],
KL [auth j],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LF [auth s],
LG [auth a],
LH [auth b],
LI [auth m],
LJ [auth l],
LL [auth j],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MG [auth a],
MH [auth b],
MI [auth m],
MK [auth i],
ML [auth j],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NF [auth s],
NG [auth a],
NI [auth m],
NK [auth i],
NL [auth j],
OA [auth A],
OC [auth B],
OD [auth B],
OG [auth a],
OI [auth m],
OK [auth i],
OL [auth j],
OM [auth d],
ON [auth Q],
PA [auth A],
PC [auth B],
PD [auth B],
PF [auth c],
PG [auth a],
PI [auth m],
PK [auth i],
QA [auth A],
QC [auth B],
QD [auth B],
QF [auth c],
QG [auth a],
QK [auth i],
QL [auth j],
RA [auth A],
RC [auth B],
RD [auth B],
RE [auth J],
RF [auth c],
RG [auth a],
RI [auth m],
RJ [auth k],
RK [auth i],
RL [auth j],
RM [auth R],
SA [auth A],
SC [auth B],
SD [auth B],
SF [auth c],
SG [auth a],
SI [auth m],
SJ [auth k],
SK [auth i],
TA [auth A],
TC [auth B],
TD [auth B],
TF [auth c],
TG [auth a],
TH [auth h],
TJ [auth k],
TK [auth i],
TM [auth n],
UA [auth A],
UC [auth B],
UD [auth B],
UF [auth c],
UH [auth h],
UJ [auth k],
UM [auth n],
VA [auth A],
VC [auth B],
VE [auth L],
VF [auth c],
VH [auth h],
VJ [auth k],
VK [auth i],
VM [auth n],
WA [auth A],
WC [auth B],
WE [auth L],
WF [auth c],
WH [auth h],
WJ [auth k],
WK [auth i],
WM [auth n],
XA [auth A],
XB [auth A],
XC [auth B],
XE [auth L],
XF [auth c],
XH [auth h],
XJ [auth k],
XM [auth n],
YA [auth A],
YB [auth A],
YC [auth B],
YH [auth h],
YJ [auth k],
YL [auth d],
YM [auth n],
ZA [auth A],
ZC [auth B],
ZE [auth L],
ZF [auth c],
ZH [auth h],
ZI [auth l],
ZJ [auth k],
ZL [auth d],
ZM [auth n]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
(Subject of Investigation/LOI)

Query on CL0



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Z [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD



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AC [auth A]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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CF [auth L]
GG [auth c]
HG [auth c]
ME [auth F]
MN [auth n]
CF [auth L],
GG [auth c],
HG [auth c],
ME [auth F],
MN [auth n],
NE [auth F],
NN [auth Q],
SH [auth b]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



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AF [auth L]
BC [auth A]
BF [auth L]
BH [auth b]
CL [auth i]
AF [auth L],
BC [auth A],
BF [auth L],
BH [auth b],
CL [auth i],
DE [auth B],
FG [auth c],
IG [auth c],
LN [auth n],
OF [auth s],
PB [auth A],
QB [auth A],
QJ [auth l],
RH [auth b],
TE [auth J],
VB [auth A],
VL [auth j],
XI [auth m]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2
(Subject of Investigation/LOI)

Query on KC2



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BK [auth k]
CK [auth k]
DK [auth k]
DL [auth i]
DN [auth n]
BK [auth k],
CK [auth k],
DK [auth k],
DL [auth i],
DN [auth n],
EN [auth n],
GF [auth s],
HM [auth d],
IM [auth d],
JF [auth s],
KJ [auth l],
PL [auth j],
QI [auth m],
UK [auth i],
YF [auth c]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II0
(Subject of Investigation/LOI)

Query on II0



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AJ [auth l]
BG [auth c]
BL [auth i]
CG [auth c]
CI [auth h]
AJ [auth l],
BG [auth c],
BL [auth i],
CG [auth c],
CI [auth h],
DI [auth h],
EG [auth c],
EI [auth h],
EL [auth i],
FK [auth k],
GK [auth k],
GN [auth n],
HK [auth k],
HN [auth n],
IK [auth k],
IN [auth n],
JK [auth k],
KK [auth k],
KM [auth d],
KN [auth n],
LM [auth d],
MJ [auth l],
MM [auth d],
NH [auth b],
NJ [auth l],
NM [auth d],
OH [auth b],
PJ [auth l],
PM [auth d],
QH [auth b],
SE [auth J],
SL [auth j],
TI [auth m],
TL [auth j],
UG [auth a],
UI [auth m],
VG [auth a],
VI [auth m],
WG [auth a],
XK [auth i],
XL [auth d],
YG [auth a],
YI [auth m],
YK [auth i],
ZK [auth i]
(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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AH [auth b]
DG [auth c]
JN [auth n]
PH [auth b]
SM [auth R]
AH [auth b],
DG [auth c],
JN [auth n],
PH [auth b],
SM [auth R],
UL [auth j],
WI [auth m],
XG [auth a]
(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
AE [auth B]
AL [auth i]
BE [auth B]
BI [auth h]
BJ [auth l]
AE [auth B],
AL [auth i],
BE [auth B],
BI [auth h],
BJ [auth l],
CE [auth B],
DC [auth A],
DF [auth M],
FE [auth B],
FF [auth K],
KE [auth F],
KF [auth s],
LE [auth F],
MF [auth s],
OE [auth I],
OJ [auth l],
PE [auth J],
QE [auth J],
QM [auth R],
RB [auth A],
SB [auth A],
TB [auth A],
UB [auth A],
UE [auth L],
XD [auth B],
YD [auth B],
YE [auth L],
ZD [auth B]
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
LMU
(Subject of Investigation/LOI)

Query on LMU



Download:Ideal Coordinates CCD File
EC [auth A],
EE [auth B],
LK [auth i],
WB [auth A],
ZG [auth a]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



Download:Ideal Coordinates CCD File
OB [auth A],
VD [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
GE [auth C],
HE [auth C],
ZB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.14 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