7WFD

Left PSI in the cyclic electron transport supercomplex NDH-PSI from Arabidopsis

  • Classification: ELECTRON TRANSPORT
  • Organism(s): Arabidopsis thaliana
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMmpstruc

  • Deposited: 2021-12-26 Released: 2022-03-16 
  • Deposition Author(s): Pan, X., Li, M.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 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

Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana.

Su, X.Cao, D.Pan, X.Shi, L.Liu, Z.Dall'Osto, L.Bassi, R.Zhang, X.Li, M.

(2022) Mol Plant 15: 454-467

  • DOI: https://doi.org/10.1016/j.molp.2022.01.020
  • Primary Citation of Related Structures:  
    7WFD, 7WFE, 7WFF, 7WFG, 7WG5

  • PubMed Abstract: 

    Cyclic electron transport/flow (CET/CEF) in chloroplasts is a regulatory process essential for the optimization of plant photosynthetic efficiency. A crucial CEF pathway is catalyzed by a membrane-embedded NADH dehydrogenase-like (NDH) complex that contains at least 29 protein subunits and associates with photosystem I (PSI) to form the NDH-PSI supercomplex. Here, we report the 3.9 Å resolution structure of the Arabidopsis thaliana NDH-PSI (AtNDH-PSI) supercomplex. We constructed structural models for 26 AtNDH subunits, among which 11 are unique to chloroplasts and stabilize the core part of the NDH complex. In the supercomplex, one NDH can bind up to two PSI-light-harvesting complex I (PSI-LHCI) complexes at both sides of its membrane arm. Two minor LHCIs, Lhca5 and Lhca6, each present in one PSI-LHCI, interact with NDH and contribute to supercomplex formation and stabilization. Collectively, our study reveals the structural details of the AtNDH-PSI supercomplex assembly and provides a molecular basis for further investigation of the regulatory mechanism of CEF in plants.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth AA]750Arabidopsis thalianaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth AB]734Arabidopsis thalianaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth AC]81Arabidopsis thalianaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P62090 (Arabidopsis thaliana)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II-2, chloroplasticD [auth AD]204Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplasticE [auth AE]143Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticF [auth AF]221Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SHE8 (Arabidopsis thaliana)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticG [auth AG]160Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9S7N7 (Arabidopsis thaliana)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI-2, chloroplasticH [auth AH]145Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SUI6 (Arabidopsis thaliana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIII [auth AI]37Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXJ [auth AJ]44Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticK [auth AK]130Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SUI5 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticL [auth AL]219Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticM [auth A1]241Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplasticN [auth A3]273Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SY97 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 4, chloroplasticO [auth A4]251Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P27521 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 6, chloroplasticP [auth A6]270Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8LCQ4 (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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ND [auth AB]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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CF [auth A1]
GH [auth A6]
HH [auth A6]
IH [auth A6]
JG [auth A3]
CF [auth A1],
GH [auth A6],
HH [auth A6],
IH [auth A6],
JG [auth A3],
NG [auth A4],
OG [auth A4],
PG [auth A4],
WF [auth A3],
XE [auth A1],
XG [auth A4]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AA
AB [auth AA]
AC [auth AB]
AD [auth AB]
AE [auth AG]
AA,
AB [auth AA],
AC [auth AB],
AD [auth AB],
AE [auth AG],
AF [auth A1],
AG [auth A3],
BA [auth AA],
BB [auth AA],
BC [auth AB],
BD [auth AB],
BE [auth AG],
BF [auth A1],
BG [auth A3],
CA [auth AA],
CB [auth AA],
CC [auth AB],
CD [auth AB],
CG [auth A3],
CH [auth A6],
DA [auth AA],
DB [auth AA],
DC [auth AB],
DD [auth AB],
DE [auth AH],
DF [auth A1],
DG [auth A3],
DH [auth A6],
EA [auth AA],
EB [auth AA],
EC [auth AB],
ED [auth AB],
EF [auth A1],
EG [auth A3],
EH [auth A6],
FA [auth AA],
FB [auth AA],
FC [auth AB],
FF [auth A1],
FH [auth A6],
GA [auth AA],
GC [auth AB],
GF [auth A1],
HA [auth AA],
HC [auth AB],
HE [auth AJ],
HF [auth A1],
IA [auth AA],
IC [auth AB],
IF [auth A1],
JA [auth AA],
JC [auth AB],
JF [auth A1],
JH [auth A6],
KA [auth AA],
KC [auth AB],
KE [auth AK],
KF [auth A1],
KG [auth A4],
KH [auth A6],
LA [auth AA],
LC [auth AB],
LG [auth A4],
LH [auth A6],
MA [auth AA],
MC [auth AB],
ME [auth AK],
MG [auth A4],
MH [auth A6],
NA [auth AA],
NC [auth AB],
NE [auth AK],
NH [auth A6],
OA [auth AA],
OC [auth AB],
OH [auth A6],
PA [auth AA],
PB [auth AB],
PC [auth AB],
Q [auth AA],
QA [auth AA],
QB [auth AB],
QC [auth AB],
QE [auth AL],
QG [auth A4],
R [auth AA],
RA [auth AA],
RB [auth AB],
RC [auth AB],
RE [auth AL],
RF [auth A3],
RG [auth A4],
S [auth AA],
SA [auth AA],
SB [auth AB],
SC [auth AB],
SE [auth AL],
SF [auth A3],
SG [auth A4],
T [auth AA],
TA [auth AA],
TB [auth AB],
TC [auth AB],
TD [auth AF],
TF [auth A3],
TG [auth A4],
U [auth AA],
UA [auth AA],
UB [auth AB],
UC [auth AB],
UD [auth AF],
UF [auth A3],
UG [auth A4],
V [auth AA],
VA [auth AA],
VB [auth AB],
VC [auth AB],
VD [auth AF],
VF [auth A3],
VG [auth A4],
W [auth AA],
WA [auth AA],
WB [auth AB],
WC [auth AB],
WG [auth A4],
X [auth AA],
XA [auth AA],
XB [auth AB],
XC [auth AB],
XF [auth A3],
Y [auth AA],
YA [auth AA],
YB [auth AB],
YC [auth AB],
YD [auth AG],
YE [auth A1],
YF [auth A3],
Z [auth AA],
ZA [auth AA],
ZB [auth AB],
ZC [auth AB],
ZE [auth A1],
ZF [auth A3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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BH [auth A4],
PF [auth A1],
ZD [auth AG]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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HB [auth AA]
IG [auth A3]
JE [auth AJ]
OF [auth A1]
QF [auth A3]
HB [auth AA],
IG [auth A3],
JE [auth AJ],
OF [auth A1],
QF [auth A3],
SH [auth A6],
VE [auth A1],
WE [auth A1]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT (Subject of Investigation/LOI)
Query on XAT

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GG [auth A3],
MF [auth A1],
QH [auth A6],
ZG [auth A4]
(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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FG [auth A3],
LF [auth A1],
PH [auth A6],
XD [auth AF],
YG [auth A4]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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AH [auth A4]
CE [auth AG]
EE [auth AI]
FE [auth AI]
GD [auth AB]
AH [auth A4],
CE [auth AG],
EE [auth AI],
FE [auth AI],
GD [auth AB],
GE [auth AJ],
HD [auth AB],
HG [auth A3],
IB [auth AA],
ID [auth AB],
IE [auth AJ],
JB [auth AA],
JD [auth AB],
KB [auth AA],
KD [auth AB],
LB [auth AA],
LD [auth AB],
LE [auth AK],
MB [auth AA],
NF [auth A1],
OE [auth AK],
RH [auth A6],
SD [auth AF],
TE [auth AL],
UE [auth AL],
WD [auth AF]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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MD [auth AB],
OB [auth AA],
OD [auth AB],
PD [auth AB],
PE [auth AL]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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FD [auth AB],
GB [auth AA]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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NB [auth AA],
QD [auth AC],
RD [auth AC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.25 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-03-16 
  • Deposition Author(s): Pan, X., Li, M.

Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0503702
Chinese Academy of SciencesChinaXDB08020106
National Natural Science Foundation of China (NSFC)China31930064
National Natural Science Foundation of China (NSFC)China31970264
National Natural Science Foundation of China (NSFC)China31770778

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary