8ZOE | pdb_00008zoe

Structure of the canthaxanthin mutant PSI-4VCPI supercomplex in Nannochloropsis oceanica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the canthaxanthin mutant PSI-4VCPI supercomplex in Nannochloropsis oceanica

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-9A [auth 9]232Nannochloropsis oceanica strain IMET1Mutation(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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-8B [auth 8]200Nannochloropsis oceanica strain IMET1Mutation(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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-7C [auth 7]202Nannochloropsis oceanica strain IMET1Mutation(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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-1D [auth 1]208Nannochloropsis oceanica strain IMET1Mutation(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: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth a]745Nannochloropsis oceanica strain IMET1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for T1RJP7 (Nannochloropsis oceanica)
Explore T1RJP7 
Go to UniProtKB:  T1RJP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RJP7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth b]737Nannochloropsis oceanica strain IMET1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for T1RIQ1 (Nannochloropsis oceanica)
Explore T1RIQ1 
Go to UniProtKB:  T1RIQ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RIQ1
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 IIG [auth d]136Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RIT2 (Nannochloropsis oceanica)
Explore T1RIT2 
Go to UniProtKB:  T1RIT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RIT2
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 IVH [auth e]67Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJT6 (Nannochloropsis oceanica)
Explore T1RJT6 
Go to UniProtKB:  T1RJT6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RJT6
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 IIII [auth f]185Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJ05 (Nannochloropsis oceanica)
Explore T1RJ05 
Go to UniProtKB:  T1RJ05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RJ05
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRJ [auth h]128Nannochloropsis oceanica strain IMET1Mutation(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: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIK [auth i]45Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJ07 (Nannochloropsis oceanica)
Explore T1RJ07 
Go to UniProtKB:  T1RJ07
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RJ07
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXL [auth j]41Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJW8 (Nannochloropsis oceanica)
Explore T1RJW8 
Go to UniProtKB:  T1RJW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RJW8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VM [auth l]172Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJZ1 (Nannochloropsis oceanica)
Explore T1RJZ1 
Go to UniProtKB:  T1RJZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RJZ1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMN [auth m]30Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for A0A8F5PPL2 (Chaetoceros tenuissimus)
Explore A0A8F5PPL2 
Go to UniProtKB:  A0A8F5PPL2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8F5PPL2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsaSO [auth g]55Nannochloropsis oceanica strain IMET1Mutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerP [auth c]81Nannochloropsis oceanica strain IMET1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for T1RJY1 (Nannochloropsis oceanica)
Explore T1RJY1 
Go to UniProtKB:  T1RJY1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupT1RJY1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

Download Ideal Coordinates CCD File 
AG [auth b],
WA [auth 8]
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 9]
AC [auth 1]
AD [auth a]
AF [auth b]
BA [auth 9]
AA [auth 9],
AC [auth 1],
AD [auth a],
AF [auth b],
BA [auth 9],
BC [auth 1],
BD [auth a],
BF [auth b],
CA [auth 9],
CB [auth 7],
CD [auth a],
CF [auth b],
DA [auth 9],
DB [auth 7],
DC [auth a],
DD [auth a],
DF [auth b],
DG [auth f],
EA [auth 9],
EB [auth 7],
EC [auth a],
ED [auth a],
EE [auth a],
EF [auth b],
EG [auth f],
FA [auth 9],
FB [auth 7],
FC [auth a],
FD [auth a],
FE [auth b],
FF [auth b],
GB [auth 7],
GC [auth a],
GD [auth a],
GE [auth b],
GF [auth b],
HA [auth 9],
HB [auth 7],
HC [auth a],
HD [auth a],
HE [auth b],
HF [auth b],
IB [auth 7],
IC [auth a],
ID [auth a],
IE [auth b],
IF [auth b],
IG [auth h],
JB [auth 7],
JC [auth a],
JD [auth a],
JE [auth b],
JF [auth b],
KB [auth 7],
KC [auth a],
KD [auth a],
KE [auth b],
KF [auth b],
KG [auth h],
LB [auth 7],
LC [auth a],
LD [auth a],
LE [auth b],
LF [auth b],
MA [auth 8],
MB [auth 7],
MC [auth a],
MD [auth a],
ME [auth b],
MF [auth b],
NA [auth 8],
NB [auth 7],
NC [auth a],
ND [auth a],
NE [auth b],
NF [auth b],
NG [auth j],
OA [auth 8],
OC [auth a],
OD [auth a],
OE [auth b],
OF [auth b],
OG [auth j],
PA [auth 8],
PC [auth a],
PD [auth a],
PE [auth b],
PF [auth b],
QA [auth 8],
QC [auth a],
QD [auth a],
QE [auth b],
QF [auth b],
RA [auth 8],
RC [auth a],
RD [auth a],
RE [auth b],
RF [auth b],
SA [auth 8],
SB [auth 1],
SC [auth a],
SD [auth a],
SE [auth b],
SF [auth b],
SG [auth l],
TA [auth 8],
TB [auth 1],
TC [auth a],
TE [auth b],
TG [auth l],
UA [auth 8],
UB [auth 1],
UC [auth a],
UD [auth a],
UE [auth b],
UG [auth l],
VA [auth 8],
VB [auth 1],
VC [auth a],
VE [auth b],
WB [auth 1],
WC [auth a],
WE [auth b],
X [auth 9],
XB [auth 1],
XC [auth a],
XE [auth b],
Y [auth 9],
YB [auth 1],
YC [auth a],
YE [auth b],
Z [auth 9],
ZB [auth 1],
ZC [auth a],
ZE [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

Download Ideal Coordinates CCD File 
CC [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

Download Ideal Coordinates CCD File 
DE [auth a],
QG [auth j]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
A1L1F (Subject of Investigation/LOI)
Query on A1L1F

Download Ideal Coordinates CCD File 
JG [auth h],
LA [auth 8],
R [auth 9],
RB [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

Download Ideal Coordinates CCD File 
GA [auth 9],
VD [auth a],
W [auth 9],
WD [auth a],
ZF [auth b]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A1L1G (Subject of Investigation/LOI)
Query on A1L1G

Download Ideal Coordinates CCD File 
OB [auth 1],
Q [auth 9],
V [auth 9],
YA [auth 7]
(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

Download Ideal Coordinates CCD File 
AB [auth 7]
BB [auth 7]
CE [auth a]
IA [auth 8]
JA [auth 8]
AB [auth 7],
BB [auth 7],
CE [auth a],
IA [auth 8],
JA [auth 8],
KA [auth 8],
MG [auth j],
PB [auth 1],
QB [auth 1],
S [auth 9],
T [auth 9],
XA [auth 7],
ZA [auth 7]
(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
45D (Subject of Investigation/LOI)
Query on 45D

Download Ideal Coordinates CCD File 
U [auth 9]beta,beta-carotene-4,4'-dione
C40 H52 O2
FDSDTBUPSURDBL-DKLMTRRASA-N
BCR (Subject of Investigation/LOI)
Query on BCR

Download Ideal Coordinates CCD File 
AE [auth a]
BG [auth b]
CG [auth f]
FG [auth f]
GG [auth h]
AE [auth a],
BG [auth b],
CG [auth f],
FG [auth f],
GG [auth h],
HG [auth h],
LG [auth i],
PG [auth j],
RG [auth l],
UF [auth b],
VF [auth b],
VG [auth l],
WF [auth b],
WG [auth m],
XD [auth a],
XF [auth b],
YD [auth a],
YF [auth b],
ZD [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.02 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