8ZOD | pdb_00008zod

Structure of the canthaxanthin mutant PSI-5VCPI supercomplex in Nannochloropsis oceanica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of the canthaxanthin mutant PSI-5VCPI supercomplex in Nannochloropsis oceanica

Shen, L.L.Li, Z.H.Shen, J.R.Wang, W.D.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-5A [auth 5]244Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-4B [auth 4]202Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-3C [auth 3]220Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-2D [auth 2]223Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-1E [auth 1]208Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1F [auth a]745Nannochloropsis oceanica strain IMET1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for T1RJP7 (Nannochloropsis oceanica)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2G [auth b]737Nannochloropsis oceanica strain IMET1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for T1RIQ1 (Nannochloropsis oceanica)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIH [auth d]136Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVI [auth e]67Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJT6 (Nannochloropsis oceanica)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIJ [auth f]185Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIK [auth i]45Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXL [auth j]41Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VM [auth l]172Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMN [auth m]30Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsaSO [auth g]55Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerP [auth c]81Nannochloropsis oceanica strain IMET1Mutation(s): 0 
EC: 1.97.1.12
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

Download Ideal Coordinates CCD File 
TG [auth b],
XA [auth 4]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth 5]
AC [auth 2]
AD [auth a]
AE [auth a]
AF [auth b]
AA [auth 5],
AC [auth 2],
AD [auth a],
AE [auth a],
AF [auth b],
AG [auth b],
AH [auth i],
BA [auth 5],
BC [auth 2],
BD [auth a],
BE [auth a],
BF [auth b],
BG [auth b],
CA [auth 5],
CC [auth 2],
CD [auth a],
CE [auth a],
CF [auth b],
CG [auth b],
CH [auth j],
DA [auth 5],
DD [auth a],
DE [auth a],
DF [auth b],
DG [auth b],
DH [auth j],
EA [auth 5],
EB [auth 3],
ED [auth a],
EE [auth a],
EF [auth b],
EG [auth b],
FB [auth 3],
FD [auth a],
FE [auth a],
FF [auth b],
FG [auth b],
GB [auth 3],
GD [auth a],
GE [auth a],
GF [auth b],
GG [auth b],
HB [auth 3],
HD [auth a],
HE [auth a],
HF [auth b],
HG [auth b],
HH [auth l],
IB [auth 3],
IC [auth 1],
ID [auth a],
IE [auth a],
IF [auth b],
IG [auth b],
IH [auth l],
JB [auth 3],
JC [auth 1],
JD [auth a],
JF [auth b],
JG [auth b],
JH [auth l],
KB [auth 3],
KC [auth 1],
KD [auth a],
KE [auth a],
KF [auth b],
LA [auth 4],
LB [auth 3],
LC [auth 1],
LD [auth a],
LF [auth b],
MA [auth 4],
MB [auth 3],
MC [auth 1],
MD [auth a],
MF [auth b],
NA [auth 4],
NC [auth 1],
ND [auth a],
NF [auth b],
OA [auth 4],
OC [auth 1],
OD [auth a],
OF [auth b],
PA [auth 4],
PC [auth 1],
PD [auth a],
PF [auth b],
QA [auth 4],
QC [auth 1],
QD [auth a],
QF [auth b],
RA [auth 4],
RC [auth 1],
RD [auth a],
RF [auth b],
SA [auth 4],
SB [auth 2],
SD [auth a],
SF [auth b],
TA [auth 4],
TB [auth 2],
TC [auth a],
TD [auth a],
TF [auth b],
U [auth 5],
UA [auth 4],
UB [auth 2],
UC [auth a],
UD [auth a],
UE [auth a],
UF [auth b],
V [auth 5],
VA [auth 4],
VB [auth 2],
VC [auth a],
VD [auth a],
VE [auth b],
VF [auth b],
W [auth 5],
WA [auth 4],
WB [auth 2],
WC [auth a],
WD [auth a],
WE [auth b],
WF [auth b],
WG [auth f],
X [auth 5],
XB [auth 2],
XC [auth a],
XD [auth a],
XE [auth b],
XF [auth b],
XG [auth f],
Y [auth 5],
YB [auth 2],
YC [auth a],
YD [auth a],
YE [auth b],
YF [auth b],
Z [auth 5],
ZB [auth 2],
ZC [auth a],
ZD [auth a],
ZE [auth b],
ZF [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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FA [auth 5],
SC [auth 1]
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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DC [auth 2],
FH [auth j],
TE [auth a]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
A1L1F (Subject of Investigation/LOI)
Query on A1L1F

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HC [auth 1][(2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E})-17-[(4~{S},6~{R})-4-acetyloxy-2,2,6-trimethyl-6-oxidanyl-cyclohexylidene]-6,11,15-trimethyl-2-[(~{E})-2-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]ethenyl]heptadeca-2,4,6,8,10,12,14,16-octaenyl] octanoate
C50 H72 O7
JYJFYJLLQQTZBJ-AYSGSIDZSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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LE [auth a],
LH [auth m],
ME [auth a],
RG [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A1L1G (Subject of Investigation/LOI)
Query on A1L1G

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DB [auth 3],
EC [auth 1],
S [auth 5],
ZA [auth 3]
(1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]-1,5,5-trimethyl-cyclohexane-1,3-diol
C40 H56 O5
OWWSPDNLRSCPIS-XZHZJERWSA-N
XAT (Subject of Investigation/LOI)
Query on XAT

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AB [auth 3]
BB [auth 3]
BH [auth j]
CB [auth 3]
FC [auth 1]
AB [auth 3],
BB [auth 3],
BH [auth j],
CB [auth 3],
FC [auth 1],
GA [auth 4],
GC [auth 1],
HA [auth 4],
IA [auth 4],
JA [auth 4],
KA [auth 4],
NB [auth 2],
OB [auth 2],
PB [auth 2],
Q [auth 5],
QB [auth 2],
R [auth 5],
RB [auth 2],
SE [auth a],
T [auth 5],
YA [auth 3]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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EH [auth j]
GH [auth l]
KH [auth l]
LG [auth b]
MG [auth b]
EH [auth j],
GH [auth l],
KH [auth l],
LG [auth b],
MG [auth b],
MH [auth m],
NE [auth a],
NG [auth b],
OE [auth a],
OG [auth b],
PE [auth a],
PG [auth b],
QE [auth a],
QG [auth b],
SG [auth b],
UG [auth b],
VG [auth f],
YG [auth f],
ZG [auth i]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
JE [auth a],
KG [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
NH [auth c],
OH [auth c],
RE [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.88 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-10
    Type: Initial release