7WFE

Right PSI in the cyclic electron transfer 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.W., Li, M.
  • Funding Organization(s): Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC), Ministry of Science and Technology (MoST, China)

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 1.0 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 BA]750Arabidopsis thalianaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth BB]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 BC]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 BD]204Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SA56 (Arabidopsis thaliana)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV A, chloroplasticE [auth BE]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 BF]221Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticG [auth BG]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 BH]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 BI]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 BJ]44Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56769 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticK [auth BK]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 BL]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 B1]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 2, chloroplasticN [auth B2]257Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SYW8 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplasticO [auth B3]273Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9SY97 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 5, chloroplasticP [auth B5]256Arabidopsis thalianaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q9C639 (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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RD [auth BB]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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AF [auth B1]
AH [auth B5]
BH [auth B5]
CG [auth B3]
IG [auth B3]
AF [auth B1],
AH [auth B5],
BH [auth B5],
CG [auth B3],
IG [auth B3],
OF [auth B2],
PF [auth B2],
QF [auth B2],
VE [auth B1],
XF [auth B2],
ZG [auth B5]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth BA]
AB [auth BA]
AC [auth BB]
AD [auth BB]
AE [auth BG]
AA [auth BA],
AB [auth BA],
AC [auth BB],
AD [auth BB],
AE [auth BG],
BA,
BB [auth BA],
BC [auth BB],
BD [auth BB],
BE [auth BG],
BF [auth B1],
CA [auth BA],
CB [auth BA],
CC [auth BB],
CD [auth BB],
CF [auth B1],
CH [auth B5],
DA [auth BA],
DB [auth BA],
DC [auth BB],
DD [auth BB],
DE [auth BH],
DF [auth B1],
DG [auth B3],
DH [auth B5],
EA [auth BA],
EB [auth BA],
EC [auth BB],
ED [auth BB],
EF [auth B1],
EG [auth B3],
EH [auth B5],
FA [auth BA],
FB [auth BA],
FC [auth BB],
FD [auth BB],
FF [auth B1],
FG [auth B3],
FH [auth B5],
GA [auth BA],
GC [auth BB],
GD [auth BB],
GF [auth B1],
GG [auth B3],
GH [auth B5],
HA [auth BA],
HB [auth BA],
HC [auth BB],
HD [auth BB],
HE [auth BJ],
HF [auth B1],
HG [auth B3],
HH [auth B5],
IA [auth BA],
IC [auth BB],
ID [auth BB],
JA [auth BA],
JC [auth BB],
JD [auth BB],
JG [auth B3],
KA [auth BA],
KC [auth BB],
KD [auth BB],
KE [auth BK],
KG [auth B3],
LA [auth BA],
LC [auth BB],
LE [auth BK],
LF [auth B2],
LG [auth B3],
MA [auth BA],
MC [auth BB],
ME [auth BK],
MF [auth B2],
MG [auth B3],
NA [auth BA],
NC [auth BB],
NF [auth B2],
NG [auth B3],
OA [auth BA],
OC [auth BB],
OG [auth B3],
PA [auth BA],
PC [auth BB],
PE [auth BL],
PG [auth B3],
Q [auth BA],
QA [auth BA],
QC [auth BB],
QE [auth BL],
QG [auth B3],
R [auth BA],
RA [auth BA],
RC [auth BB],
RE [auth BL],
RF [auth B2],
S [auth BA],
SA [auth BA],
SC [auth BB],
SF [auth B2],
T [auth BA],
TA [auth BA],
TC [auth BB],
TF [auth B2],
U [auth BA],
UA [auth BA],
UB [auth BB],
UC [auth BB],
UF [auth B2],
V [auth BA],
VA [auth BA],
VB [auth BB],
VC [auth BB],
VD [auth BF],
VF [auth B2],
VG [auth B5],
W [auth BA],
WA [auth BA],
WC [auth BB],
WD [auth BF],
WE [auth B1],
WF [auth B2],
WG [auth B5],
X [auth BA],
XA [auth BA],
XB [auth BB],
XC [auth BB],
XD [auth BF],
XE [auth B1],
XG [auth B5],
Y [auth BA],
YA [auth BA],
YB [auth BB],
YC [auth BB],
YE [auth B1],
YG [auth B5],
Z [auth BA],
ZA [auth BA],
ZB [auth BB],
ZC [auth BB],
ZE [auth B1]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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JE [auth BJ]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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LH [auth B5]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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BG [auth B2]
IB [auth BA]
JB [auth BA]
KF [auth B1]
MH [auth B5]
BG [auth B2],
IB [auth BA],
JB [auth BA],
KF [auth B1],
MH [auth B5],
TE [auth B1],
UE [auth B1],
UG [auth B3],
ZD [auth BF]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT (Subject of Investigation/LOI)
Query on XAT

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JF [auth B1],
JH [auth B5],
SG [auth B3],
ZF [auth B2]
(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 (Subject of Investigation/LOI)
Query on LUT

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IF [auth B1],
IH [auth B5],
RG [auth B3],
YF [auth B2]
(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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AG [auth B2]
CE [auth BG]
EE [auth BH]
FE [auth BI]
GE [auth BJ]
AG [auth B2],
CE [auth BG],
EE [auth BH],
FE [auth BI],
GE [auth BJ],
IE [auth BJ],
KB [auth BA],
KH [auth B5],
LB [auth BA],
MB [auth BA],
MD [auth BB],
NB [auth BA],
ND [auth BB],
NE [auth BK],
OB [auth BA],
OD [auth BB],
OE [auth BL],
PD [auth BB],
QD [auth BB],
SB [auth BA],
SE [auth BL],
TB [auth BA],
TG [auth B3],
WB [auth BB],
YD [auth BF]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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QB [auth BA],
RB [auth BA],
SD [auth BB]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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GB [auth BA],
LD [auth BB]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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PB [auth BA],
TD [auth BC],
UD [auth BC]
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


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB27020106
National Natural Science Foundation of China (NSFC)China31930064
National Natural Science Foundation of China (NSFC)China31970264
National Natural Science Foundation of China (NSFC)China31770778
Ministry of Science and Technology (MoST, China)China2017YFA0503702

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-16
    Type: Initial release