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


This is version 1.1 of the entry. See complete history


Literature

Regulatory dynamics of the higher-plant PSI-LHCI supercomplex during state transitions.

Wu, J.Chen, S.Wang, C.Lin, W.Huang, C.Fan, C.Han, D.Lu, D.Xu, X.Sui, S.Zhang, L.

(2023) Mol Plant 16: 1937-1950

  • DOI: https://doi.org/10.1016/j.molp.2023.11.002
  • Primary Citation of Related Structures:  
    8J6Z, 8J7A, 8J7B

  • PubMed Abstract: 

    State transition is a fundamental light acclimation mechanism of photosynthetic organisms in response to the environmental light conditions. This process rebalances the excitation energy between photosystem I (PSI) and photosystem II through regulated reversible binding of the light-harvesting complex II (LHCII) to PSI. However, the structural reorganization of PSI-LHCI, the dynamic binding of LHCII, and the regulatory mechanisms underlying state transitions are less understood in higher plants. In this study, using cryoelectron microscopy we resolved the structures of PSI-LHCI in both state 1 (PSI-LHCI-ST1) and state 2 (PSI-LHCI-LHCII-ST2) from Arabidopsis thaliana. Combined genetic and functional analyses revealed novel contacts between Lhcb1 and PsaK that further enhanced the binding of the LHCII trimer to the PSI core with the known interactions between phosphorylated Lhcb2 and the PsaL/PsaH/PsaO subunits. Specifically, PsaO was absent in the PSI-LHCI-ST1 supercomplex but present in the PSI-LHCI-LHCII-ST2 supercomplex, in which the PsaL/PsaK/PsaA subunits undergo several conformational changes to strengthen the binding of PsaO in ST2. Furthermore, the PSI-LHCI module adopts a more compact configuration with shorter Mg-to-Mg distances between the chlorophylls, which may enhance the energy transfer efficiency from the peripheral antenna to the PSI core in ST2. Collectively, our work provides novel structural and functional insights into the mechanisms of light acclimation during state transitions in higher plants.


  • Organizational Affiliation

    State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Jinming Avenue, Kaifeng 475004, China.


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 
UniProt
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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
  • Version 1.1: 2024-05-29
    Changes: Database references