7WFF

Subcomplexes B,M and L in the Cylic electron transfer supercomplex NDH-PSI from Arabidopsis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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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: 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 ...

    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. Electronic address: meili@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 1, chloroplasticA360Arabidopsis thalianaMutation(s): 0 
Gene Names: ndhAAtCg01100
EC: 7.1.1
Membrane Entity: Yes 
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Find proteins for Q37165 (Arabidopsis thaliana)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 2, chloroplasticB512Arabidopsis thalianaMutation(s): 0 
Gene Names: ndhB
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for A0A1B1W4Z4 (Arabidopsis thaliana)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 3, chloroplasticC120Arabidopsis thalianaMutation(s): 0 
Gene Names: ndhCAtCg00440
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase chain 4, chloroplasticD506Arabidopsis thalianaMutation(s): 0 
Gene Names: ndhD
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 4L, chloroplasticE101Arabidopsis thalianaMutation(s): 0 
Gene Names: ndhEAtCg01070
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 5, chloroplasticF746Arabidopsis thalianaMutation(s): 0 
Gene Names: ndhFAtCg01010
EC: 7.1.1
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 6, chloroplasticG176Arabidopsis thalianaMutation(s): 0 
Gene Names: ndhGAtCg01080
EC: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 1, chloroplasticH [auth a]461Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSB1GT9NDF1NDH48At1g15980T24D18.8
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 2, chloroplasticI [auth b]348Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSB2NDF2NDH45At1g64770F13O11.8
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 3, chloroplasticJ [auth c]204Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSB3NDF4At3g16250MYA6.6
Membrane Entity: Yes 
UniProt
Find proteins for Q9LU21 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NDH dependent flow 6K [auth d]161Arabidopsis thalianaMutation(s): 0 
Gene Names: PnsB4NDF6NDH dependent flow 6At1g18730F6A14.16F6A14_16
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of subcomplex B 5, chloroplasticL [auth e]212Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSB5NDH18At5g43750MQD19.9
Membrane Entity: Yes 
UniProt
Find proteins for Q9FG89 (Arabidopsis thaliana)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 1, chloroplasticM [auth f]238Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSL1PPL2At2g39470F12L6.13
Membrane Entity: Yes 
UniProt
Find proteins for O80634 (Arabidopsis thaliana)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 2, chloroplasticN [auth g]190Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSL2PQL1PQL2At1g14150F7A19.23
Membrane Entity: Yes 
UniProt
Find proteins for Q9XI73 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 3, chloroplasticO [auth h]220Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSL3PQL1PQL2At3g01440T13O15.8
Membrane Entity: Yes 
UniProt
Find proteins for Q9SGH4 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Photosynthetic NDH subunit of lumenal location 4, chloroplasticP [auth i]217Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSL4FKBP16-2FKBP22-2FKBP23IAt4g39710T19P19.100
EC: 5.2.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q9SCY3 (Arabidopsis thaliana)
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of Photosynthetic NDH subunit of lumenal location 5, chloroplasticQ [auth j]255Arabidopsis thalianaMutation(s): 0 
Gene Names: PNSL5CYP20-2At5g13120T19L5_80
EC: 5.2.1.8
Membrane Entity: Yes 
UniProt
Find proteins for Q9ASS6 (Arabidopsis thaliana)
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SQD
Query on SQD

Download Ideal Coordinates CCD File 
T [auth F]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
LHG
Query on LHG

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R [auth D],
S [auth F]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
FES (Subject of Investigation/LOI)
Query on FES

Download Ideal Coordinates CCD File 
U [auth c]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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