8J7B

Coordinates of Cryo-EM structure of the Arabidopsis thaliana PSI in state 2 (PSI-ST2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Cryo-EM structure of the Arabidopsis thaliana photosystem I(PSI-LHCII-ST2)

Chen, S.J.B.Wu, J.H.Sui, S.F.Zhang, L.X.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticA [auth 1]241Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA1CAB6At3g54890F28P10.130
Membrane Entity: Yes 
UniProt
Find proteins for Q01667 (Arabidopsis thaliana)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 2, chloroplasticB [auth 2]257Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA2At3g61470F2A19.70
Membrane Entity: Yes 
UniProt
Find proteins for Q9SYW8 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplasticC [auth 3]273Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA3At1g61520T25B24.12
Membrane Entity: Yes 
UniProt
Find proteins for Q9SY97 (Arabidopsis thaliana)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 4, chloroplasticD [auth 4]251Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA4CAB4At3g47470F1P2.20
Membrane Entity: Yes 
UniProt
Find proteins for P27521 (Arabidopsis thaliana)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]750Arabidopsis thalianaMutation(s): 0 
Gene Names: psaAAtCg00350
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P56766 (Arabidopsis thaliana)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Arabidopsis thalianaMutation(s): 0 
Gene Names: psaBAtCg00340
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Arabidopsis thalianaMutation(s): 0 
Gene Names: psaCfrxAAtCg01060
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P62090 (Arabidopsis thaliana)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II-2, chloroplasticH [auth D]204Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAD2At1g03130F10O3_4
Membrane Entity: Yes 
UniProt
Find proteins for Q9SA56 (Arabidopsis thaliana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplasticI [auth E]143Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAE1At4g28750F16A16.140
Membrane Entity: Yes 
UniProt
Find proteins for Q9S831 (Arabidopsis thaliana)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticJ [auth F]221Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAFAt1g31330T19E23.12
Membrane Entity: Yes 
UniProt
Find proteins for Q9SHE8 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticK [auth G]160Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAGAt1g55670F20N2.21F20N2.33F20N2_3
Membrane Entity: Yes 
UniProt
Find proteins for Q9S7N7 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI-2, chloroplasticL [auth H]145Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAH2At1g52230F9I5.11
Membrane Entity: Yes 
UniProt
Find proteins for Q9SUI6 (Arabidopsis thaliana)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]37Arabidopsis thalianaMutation(s): 0 
Gene Names: psaIAtCg00510
Membrane Entity: Yes 
UniProt
Find proteins for P56768 (Arabidopsis thaliana)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]44Arabidopsis thalianaMutation(s): 0 
Gene Names: psaJAtCg00630
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticO [auth K]130Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAKAt1g30380T4K22.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9SUI5 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticP [auth L]219Arabidopsis thalianaMutation(s): 0 
Gene Names: PSALAt4g12800T20K18.150
Membrane Entity: Yes 
UniProt
Find proteins for Q9SUI4 (Arabidopsis thaliana)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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IG [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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GA [auth 2]
HA [auth 2]
JA [auth 2]
NA [auth 2]
NB [auth 4]
GA [auth 2],
HA [auth 2],
JA [auth 2],
NA [auth 2],
NB [auth 4],
Q [auth 1],
QA [auth 2],
RB [auth 4],
UB [auth 4],
V [auth 1],
YB [auth 4],
ZA [auth 3]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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PC [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth 1]
AB [auth 3]
AC [auth 4]
AD [auth A]
AE [auth A]
AA [auth 1],
AB [auth 3],
AC [auth 4],
AD [auth A],
AE [auth A],
AF [auth B],
AH [auth K],
BA [auth 1],
BB [auth 3],
BC [auth 4],
BD [auth A],
BE [auth A],
BF [auth B],
BG [auth B],
BH [auth K],
CA [auth 1],
CB [auth 3],
CC [auth 4],
CE [auth A],
CF [auth B],
DB [auth 3],
DC [auth 4],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
EB [auth 3],
EC [auth 4],
ED [auth A],
EE [auth A],
EF [auth B],
EH [auth L],
FB [auth 3],
FC [auth 4],
FD [auth A],
GB [auth 3],
GC [auth A],
GD [auth A],
GE [auth A],
GF [auth B],
GG [auth B],
HC [auth A],
HD [auth A],
HE [auth A],
HF [auth B],
HG [auth B],
HH [auth L],
IA [auth 2],
IB [auth 3],
IC [auth A],
IE [auth A],
IH [auth L],
JC [auth A],
JF [auth B],
KB [auth 3],
KC [auth A],
KD [auth A],
KF [auth B],
LA [auth 2],
LB [auth 3],
LC [auth A],
LG [auth F],
MC [auth A],
MD [auth A],
ME [auth B],
MF [auth B],
NC [auth A],
NE [auth B],
NF [auth B],
NG [auth F],
OA [auth 2],
OB [auth 4],
OC [auth A],
OE [auth B],
OF [auth B],
OG [auth F],
PA [auth 2],
PB [auth 4],
PD [auth A],
PE [auth B],
PF [auth B],
PG [auth G],
QC [auth A],
QD [auth A],
QE [auth B],
QF [auth B],
QG [auth G],
R [auth 1],
RA [auth 2],
RC [auth A],
RD [auth A],
RE [auth B],
RF [auth B],
S [auth 1],
SB [auth 4],
SC [auth A],
SD [auth A],
SE [auth B],
SF [auth B],
SG [auth G],
T [auth 1],
TA [auth 2],
TC [auth A],
TE [auth B],
TF [auth B],
TG [auth H],
U [auth 1],
UC [auth A],
UD [auth A],
UE [auth B],
UF [auth B],
VA [auth 2],
VC [auth A],
VE [auth B],
W [auth 1],
WA [auth 2],
WB [auth 4],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
WG [auth J],
X [auth 1],
XA [auth 2],
XC [auth A],
XD [auth A],
XE [auth B],
XF [auth B],
XG [auth K],
Y [auth 1],
YA [auth 3],
YC [auth A],
YE [auth B],
YF [auth B],
YG [auth K],
Z [auth 1],
ZB [auth 4],
ZC [auth A],
ZD [auth A],
ZE [auth B],
ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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VB [auth 4],
XB [auth 4]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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EA [auth 1]
JD [auth A]
LF [auth B]
UA [auth 2]
VD [auth A]
EA [auth 1],
JD [auth A],
LF [auth B],
UA [auth 2],
VD [auth A],
VF [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

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DA [auth 1],
MB [auth 4],
SA [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
LUT
Query on LUT

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FA [auth 1],
HB [auth 3],
KA [auth 2],
MA [auth 2],
QB [auth 4]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

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AG [auth B]
CD [auth A]
CG [auth B]
CH [auth K]
DH [auth L]
AG [auth B],
CD [auth A],
CG [auth B],
CH [auth K],
DH [auth L],
EG [auth B],
FE [auth A],
FF [auth B],
FG [auth B],
FH [auth L],
GH [auth L],
ID [auth A],
JB [auth 3],
JE [auth B],
KE [auth B],
LD [auth A],
LE [auth B],
MG [auth F],
RG [auth G],
TB [auth 4],
TD [auth A],
UG [auth I],
VG [auth J],
YD [auth A],
ZG [auth K]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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IF [auth B],
ND [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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JG [auth C],
KG [auth C],
OD [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.22 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-15
    Type: Initial release