8J6Z

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 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

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

Chen, S.J.B.Wu, J.H.

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 
UniProt
Find proteins for P56767 (Arabidopsis thaliana)
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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
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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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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit OQ [auth O]140Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAOAt1g08380T27G7
Membrane Entity: Yes 
UniProt
Find proteins for Q949Q5 (Arabidopsis thaliana)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2, chloroplasticR [auth x],
S [auth y]
267Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCB1.1AB165CAB2LHCP-BAt1g29920F1N18.4
Membrane Entity: Yes 
UniProt
Find proteins for P0CJ48 (Arabidopsis thaliana)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2.1, chloroplasticT [auth z]265Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCB2.1LHCB2.3At2g05100F15L11.2
Membrane Entity: Yes 
UniProt
Find proteins for Q9SHR7 (Arabidopsis thaliana)
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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

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BI [auth x]
BJ [auth y]
CJ [auth y]
DI [auth x]
IB [auth 3]
BI [auth x],
BJ [auth y],
CJ [auth y],
DI [auth x],
IB [auth 3],
IC [auth 4],
JJ [auth z],
LJ [auth z],
MI [auth y],
MJ [auth z],
NA [auth 2],
OA [auth 2],
OI [auth y],
OJ [auth z],
PA [auth 2],
PI [auth y],
QB [auth 4],
RA [auth 2],
RB [auth 4],
SH [auth x],
SJ [auth z],
TH [auth x],
U [auth 1],
UH [auth x],
VA [auth 2],
VI [auth y],
WJ [auth z],
XB [auth 4],
XH [auth x],
Z [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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LD [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 2]
AD [auth A]
AE [auth A]
AF [auth B]
AA [auth 1],
AB [auth 2],
AD [auth A],
AE [auth A],
AF [auth B],
AG [auth B],
AH [auth J],
AI [auth x],
BA [auth 1],
BC [auth 4],
BD [auth A],
BE [auth A],
CA [auth 1],
CB [auth 3],
CD [auth A],
CE [auth A],
CH [auth K],
CI [auth x],
DA [auth 1],
DB [auth 3],
DC [auth 4],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
DH [auth K],
DJ [auth y],
EA [auth 1],
EB [auth 3],
EC [auth 4],
ED [auth A],
EF [auth B],
EG [auth B],
EI [auth x],
EJ [auth z],
FA [auth 1],
FB [auth 3],
FC [auth 4],
FD [auth A],
FE [auth A],
FF [auth B],
FG [auth B],
FH [auth K],
FI [auth x],
FJ [auth z],
GA [auth 1],
GB [auth 3],
GC [auth 4],
GD [auth A],
GF [auth B],
GG [auth B],
GH [auth K],
GI [auth x],
GJ [auth z],
HB [auth 3],
HD [auth A],
HF [auth B],
HG [auth B],
HH [auth L],
HJ [auth z],
ID [auth A],
IE [auth A],
IF [auth B],
IG [auth B],
IH [auth L],
IJ [auth z],
JB [auth 3],
JC [auth 4],
JD [auth A],
JE [auth A],
JF [auth B],
JG [auth B],
JH [auth L],
KA [auth 2],
KC [auth A],
KD [auth A],
KF [auth B],
KI [auth x],
LA [auth 2],
LB [auth 3],
LC [auth A],
LE [auth A],
LF [auth B],
LG [auth B],
LI [auth y],
MA [auth 2],
MC [auth A],
MD [auth A],
ME [auth A],
MF [auth B],
MG [auth B],
NB [auth 3],
NC [auth A],
ND [auth A],
NE [auth B],
NF [auth B],
NH [auth O],
NI [auth y],
OB [auth 3],
OC [auth A],
OD [auth A],
OE [auth B],
OF [auth B],
OH [auth O],
PB [auth 3],
PC [auth A],
PE [auth B],
PF [auth B],
PG [auth F],
PJ [auth z],
QA [auth 2],
QC [auth A],
QD [auth A],
QE [auth B],
QF [auth B],
QG [auth F],
QI [auth y],
QJ [auth z],
RC [auth A],
RE [auth B],
RF [auth B],
RG [auth F],
RH [auth O],
SA [auth 2],
SC [auth A],
SD [auth A],
SE [auth B],
SF [auth B],
SI [auth y],
TA [auth 2],
TB [auth 4],
TC [auth A],
TE [auth B],
TG [auth G],
TI [auth y],
UC [auth A],
UE [auth B],
UG [auth G],
UI [auth y],
UJ [auth z],
V [auth 1],
VB [auth 4],
VC [auth A],
VD [auth A],
VE [auth B],
W [auth 1],
WB [auth 4],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
WG [auth G],
WH [auth x],
WI [auth y],
X [auth 1],
XA [auth 2],
XC [auth A],
XD [auth A],
XE [auth B],
XG [auth H],
Y [auth 1],
YB [auth 4],
YC [auth A],
ZA [auth 2],
ZB [auth 4],
ZC [auth A],
ZE [auth B],
ZH [auth x]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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

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AJ [auth y]
BB [auth 2]
BG [auth B]
CG [auth B]
EE [auth A]
AJ [auth y],
BB [auth 2],
BG [auth B],
CG [auth B],
EE [auth A],
IA [auth 1],
JI [auth x],
KE [auth A],
RJ [auth z]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
Query on NEX

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II [auth x],
VJ [auth z],
ZI [auth y]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
XAT
Query on XAT

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HA [auth 1]
HI [auth x]
NJ [auth z]
UB [auth 4]
YA [auth 2]
HA [auth 1],
HI [auth x],
NJ [auth z],
UB [auth 4],
YA [auth 2],
YI [auth y]
(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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JA [auth 1]
KB [auth 3]
KJ [auth z]
RI [auth y]
SB [auth 4]
JA [auth 1],
KB [auth 3],
KJ [auth z],
RI [auth y],
SB [auth 4],
TJ [auth z],
UA [auth 2],
VH [auth x],
WA [auth 2],
XI [auth y],
YH [auth x]
(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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AC [auth 4]
BH [auth K]
CF [auth B]
EH [auth K]
KG [auth B]
AC [auth 4],
BH [auth K],
CF [auth B],
EH [auth K],
KG [auth B],
KH [auth L],
LH [auth L],
MB [auth 3],
MH [auth L],
PD [auth A],
PH [auth O],
QH [auth O],
RD [auth A],
SG [auth F],
TD [auth A],
TF [auth B],
UD [auth A],
UF [auth B],
VF [auth B],
VG [auth G],
XF [auth B],
YD [auth A],
YE [auth B],
YF [auth B],
YG [auth I],
ZD [auth A],
ZG [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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

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GE [auth A],
NG [auth C],
OG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
T [auth z]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



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