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

Validation slider image for 9L5V

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: 1,145.72 kDa 
  • Atom Count: 69,223 
  • Modeled Residue Count: 6,430 
  • Deposited Residue Count: 7,928 
  • Unique protein chains: 24

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Q [auth a]
374Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for A6MVT2 (Rhodomonas salina)
Explore A6MVT2 
Go to UniProtKB:  A6MVT2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVT2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
R [auth b]
508Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MW31 (Rhodomonas salina)
Explore A6MW31 
Go to UniProtKB:  A6MW31
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MW31
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
S [auth c]
486Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVR2 (Rhodomonas salina)
Explore A6MVR2 
Go to UniProtKB:  A6MVR2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVR2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
T [auth d]
351Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for A6MVR3 (Rhodomonas salina)
Explore A6MVR3 
Go to UniProtKB:  A6MVR3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVR3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
U [auth e]
84Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVV5 (Rhodomonas salina)
Explore A6MVV5 
Go to UniProtKB:  A6MVV5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVV5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
V [auth f]
42Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVV4 (Rhodomonas salina)
Explore A6MVV4 
Go to UniProtKB:  A6MVV4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVV4
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
W [auth h]
67Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MW35 (Rhodomonas salina)
Explore A6MW35 
Go to UniProtKB:  A6MW35
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MW35
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
X [auth i]
38Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVW0 (Rhodomonas salina)
Explore A6MVW0 
Go to UniProtKB:  A6MVW0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVW0
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KI [auth K],
Y [auth k]
45Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVZ3 (Rhodomonas salina)
Explore A6MVZ3 
Go to UniProtKB:  A6MVZ3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVZ3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJ [auth L],
Z [auth l]
38Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVV3 (Rhodomonas salina)
Explore A6MVV3 
Go to UniProtKB:  A6MVV3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVV3
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein MAA [auth m],
K [auth M]
118Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TBA [auth t],
L [auth T]
32Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MW32 (Rhodomonas salina)
Explore A6MW32 
Go to UniProtKB:  A6MW32
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MW32
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein WCA [auth w],
M [auth W]
121Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinDA [auth x],
N [auth X]
39Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVU5 (Rhodomonas salina)
Explore A6MVU5 
Go to UniProtKB:  A6MVU5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVU5
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Psb30EA [auth y],
O [auth Y]
34Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVU9 (Rhodomonas salina)
Explore A6MVU9 
Go to UniProtKB:  A6MVU9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVU9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZFA [auth z],
P [auth Z]
62Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVZ2 (Rhodomonas salina)
Explore A6MVZ2 
Go to UniProtKB:  A6MVZ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVZ2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPII-1GA [auth 1],
HA [auth N]
234Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPII-2IA [auth 2],
OA [auth O]
215Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPII-3JA [auth 3],
PA [auth P]
182Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPII-4KA [auth 4],
QA [auth Q]
200Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPII-5LA [auth 5],
RA [auth R]
228Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
ACPII-6MA [auth 6],
SA [auth S]
174Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
Psb-gama_linkerNA [auth G]292Rhodomonas sp. NIES-2332Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Psb-gama_linkerTA [auth g]292Rhodomonas sp. NIES-2332Mutation(s): 0 

Small Molecules

Ligands 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
PD [auth a],
UA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
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