8ZOA | pdb_00008zoa

Structure of the wild-type PSI-8VCPI supercomplex in Nannochloropsis oceanica


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure of the wild-type PSI-8VCPI 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-9B [auth 9]232Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-8C [auth 8]200Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-4/7D [auth 4],
G [auth 7]
202Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-3E [auth 3]220Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-2F [auth 2]223Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
VCPI-1H [auth 1]208Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1I [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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2J [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: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIK [auth d]136Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RIT2 (Nannochloropsis oceanica)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVL [auth e]67Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJT6 (Nannochloropsis oceanica)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIM [auth f]185Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJ05 (Nannochloropsis oceanica)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRN [auth h]128Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIO [auth i]45Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJ07 (Nannochloropsis oceanica)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXP [auth j]41Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJW8 (Nannochloropsis oceanica)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VQ [auth l]172Nannochloropsis oceanica strain IMET1Mutation(s): 0 
UniProt
Find proteins for T1RJZ1 (Nannochloropsis oceanica)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMR [auth m]30Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsaSS [auth g]55Nannochloropsis oceanica strain IMET1Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerT [auth c]81Nannochloropsis oceanica strain IMET1Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for T1RJY1 (Nannochloropsis oceanica)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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IC [auth 4],
QB [auth 8],
SI [auth b]
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 4]
AE [auth 7]
AF [auth a]
AG [auth a]
AA [auth 5],
AC [auth 4],
AE [auth 7],
AF [auth a],
AG [auth a],
AH [auth b],
AI [auth b],
AJ [auth h],
BA [auth 5],
BB [auth 9],
BC [auth 4],
BE [auth 7],
BF [auth a],
BG [auth a],
BH [auth b],
BI [auth b],
CA [auth 5],
CC [auth 4],
CE [auth 7],
CF [auth a],
CG [auth a],
CH [auth b],
CI [auth b],
CJ [auth h],
DA [auth 5],
DC [auth 4],
DD [auth 2],
DE [auth 7],
DF [auth a],
DG [auth a],
DH [auth b],
DI [auth b],
EA [auth 5],
EC [auth 4],
ED [auth 2],
EE [auth 7],
EF [auth a],
EG [auth a],
EH [auth b],
EI [auth b],
FA [auth 5],
FC [auth 4],
FD [auth 2],
FE [auth 7],
FF [auth a],
FG [auth a],
FH [auth b],
FI [auth b],
FJ [auth j],
GA [auth 5],
GB [auth 8],
GC [auth 4],
GD [auth 2],
GF [auth a],
GG [auth a],
GH [auth b],
GI [auth b],
GJ [auth j],
HA [auth 5],
HB [auth 8],
HC [auth 4],
HD [auth 2],
HF [auth a],
HG [auth a],
HH [auth b],
HI [auth b],
IA [auth 5],
IB [auth 8],
ID [auth 2],
IF [auth a],
IG [auth a],
IH [auth b],
II [auth b],
JB [auth 8],
JD [auth 2],
JF [auth a],
JG [auth a],
JH [auth b],
JI [auth b],
KB [auth 8],
KD [auth 2],
KE [auth 1],
KF [auth a],
KG [auth a],
KH [auth b],
KI [auth b],
KJ [auth l],
LB [auth 8],
LD [auth 2],
LE [auth 1],
LF [auth a],
LH [auth b],
LJ [auth l],
MB [auth 8],
MD [auth 2],
ME [auth 1],
MF [auth a],
MG [auth a],
MH [auth b],
MJ [auth l],
NB [auth 8],
ND [auth 2],
NE [auth 1],
NF [auth a],
NH [auth b],
OB [auth 8],
OE [auth 1],
OF [auth a],
OH [auth b],
PB [auth 8],
PC [auth 3],
PE [auth 1],
PF [auth a],
PH [auth b],
QC [auth 3],
QE [auth 1],
QF [auth a],
QH [auth b],
RA [auth 9],
RC [auth 3],
RE [auth 1],
RF [auth a],
RH [auth b],
SA [auth 9],
SC [auth 3],
SE [auth 1],
SF [auth a],
SH [auth b],
TA [auth 9],
TC [auth 3],
TE [auth 1],
TF [auth a],
TH [auth b],
UA [auth 9],
UC [auth 3],
UD [auth 7],
UF [auth a],
UH [auth b],
VA [auth 9],
VC [auth 3],
VD [auth 7],
VE [auth a],
VF [auth a],
VH [auth b],
VI [auth f],
WA [auth 9],
WB [auth 4],
WC [auth 3],
WD [auth 7],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth b],
WI [auth f],
XA [auth 9],
XB [auth 4],
XC [auth 3],
XD [auth 7],
XE [auth a],
XF [auth a],
XG [auth b],
XH [auth b],
Y [auth 5],
YA [auth 9],
YB [auth 4],
YD [auth 7],
YE [auth a],
YF [auth a],
YG [auth b],
YH [auth b],
Z [auth 5],
ZA [auth 9],
ZB [auth 4],
ZD [auth 7],
ZE [auth a],
ZF [auth a],
ZG [auth b],
ZH [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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JA [auth 5],
UE [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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IJ [auth j],
OD [auth 2],
VG [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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BJ [auth h],
FB [auth 8],
JE [auth 1],
LA [auth 9]
[(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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AB [auth 9],
NG [auth a],
OG [auth a],
QA [auth 9],
RI [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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GE [auth 1]
KA [auth 9]
KC [auth 3]
OC [auth 3]
PA [auth 9]
GE [auth 1],
KA [auth 9],
KC [auth 3],
OC [auth 3],
PA [auth 9],
QD [auth 7],
W [auth 5]
(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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AD [auth 2]
BD [auth 2]
CB [auth 8]
CD [auth 2]
DB [auth 8]
AD [auth 2],
BD [auth 2],
CB [auth 8],
CD [auth 2],
DB [auth 8],
EB [auth 8],
EJ [auth j],
HE [auth 1],
IE [auth 1],
JC [auth 3],
LC [auth 3],
MA [auth 9],
MC [auth 3],
NA [auth 9],
NC [auth 3],
OA [auth 9],
PD [auth 7],
RB [auth 4],
RD [auth 7],
SB [auth 4],
SD [auth 7],
TB [auth 4],
TD [auth 7],
U [auth 5],
UB [auth 4],
UG [auth a],
V [auth 5],
VB [auth 4],
X [auth 5],
YC [auth 2],
ZC [auth 2]
(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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DJ [auth i]
HJ [auth j]
JJ [auth l]
MI [auth b]
NI [auth b]
DJ [auth i],
HJ [auth j],
JJ [auth l],
MI [auth b],
NI [auth b],
NJ [auth l],
OI [auth b],
OJ [auth m],
PG [auth a],
PI [auth b],
QG [auth a],
QI [auth b],
RG [auth a],
SG [auth a],
TI [auth b],
UI [auth f],
XI [auth f],
YI [auth h],
ZI [auth h]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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LG [auth a],
LI [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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PJ [auth c],
QJ [auth c],
TG [auth a]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release