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 

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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1752Rhodomonas sp. NIES-2332Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for O78508 (Guillardia theta)
Explore O78508 
Go to UniProtKB:  O78508
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO78508
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A6MVZ6 
Go to UniProtKB:  A6MVZ6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVZ6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A6MVS8 
Go to UniProtKB:  A6MVS8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVS8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II141Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVZ1 (Rhodomonas salina)
Explore A6MVZ1 
Go to UniProtKB:  A6MVZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVZ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV64Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MW36 (Rhodomonas salina)
Explore A6MW36 
Go to UniProtKB:  A6MW36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MW36
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III188Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVU7 (Rhodomonas salina)
Explore A6MVU7 
Go to UniProtKB:  A6MVU7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVU7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVV1 (Rhodomonas salina)
Explore A6MVV1 
Go to UniProtKB:  A6MVV1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVV1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A6MVU6 
Go to UniProtKB:  A6MVU6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVU6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A6MVV8 
Go to UniProtKB:  A6MVV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVV8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A6MVT4 
Go to UniProtKB:  A6MVT4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVT4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaK87Rhodomonas sp. NIES-2332Mutation(s): 0 
UniProt
Find proteins for A6MVS9 (Rhodomonas salina)
Explore A6MVS9 
Go to UniProtKB:  A6MVS9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6MVS9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-sL [auth s]302Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-cM [auth c]215Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-aN [auth a]217Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-bO [auth b]236Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-hP [auth h]229Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-mQ [auth m],
U [auth j]
212Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-lR [auth l]175Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-kS [auth k]232Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-iT [auth i]200Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-dV [auth d]219Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRW [auth R]135Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-nX [auth n]220Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
PsaQY [auth Q]233Rhodomonas sp. NIES-2332Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
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

Download Ideal Coordinates CCD File 
Z [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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

Download Ideal Coordinates CCD File 
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