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- PDB-7wfe: Right PSI in the cyclic electron transfer supercomplex NDH-PSI fr... -

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Basic information

Entry
Database: PDB / ID: 7wfe
TitleRight PSI in the cyclic electron transfer supercomplex NDH-PSI from Arabidopsis
Components
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I chlorophyll a/b-binding protein ...) x 3
  • (Photosystem I reaction center subunit ...) x 9
  • Chlorophyll a-b binding protein 6, chloroplastic
  • Photosystem I iron-sulfur center
KeywordsELECTRON TRANSPORT / Cylic electron trasport / supercomplex / Arabidopsis / plant
Function / homology
Function and homology information


photosystem I antenna complex / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus / chloroplast stromal thylakoid / pigment binding / plastoglobule / chloroplast membrane / response to high light intensity ...photosystem I antenna complex / photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus / chloroplast stromal thylakoid / pigment binding / plastoglobule / chloroplast membrane / response to high light intensity / chloroplast thylakoid / photosynthesis, light harvesting in photosystem I / thylakoid / chloroplast envelope / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / plastid / chlorophyll binding / chloroplast thylakoid membrane / photosynthesis / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / protein homodimerization activity / extracellular region / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK ...Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / 4Fe-4S dicluster domain / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I reaction centre subunit PsaK superfamily / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / : / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-SQD / Chem-XAT / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein 6, chloroplastic / Photosystem I chlorophyll a/b-binding protein 5, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit IV A, chloroplastic / Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit VI-2, chloroplastic / Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsPan, X.W. / Li, M.
Funding support China, 5items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)31930064 China
National Natural Science Foundation of China (NSFC)31970264 China
National Natural Science Foundation of China (NSFC)31770778 China
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
CitationJournal: Mol Plant / Year: 2022
Title: Supramolecular assembly of chloroplast NADH dehydrogenase-like complex with photosystem I from Arabidopsis thaliana.
Authors: Xiaodong Su / Duanfang Cao / Xiaowei Pan / Lifang Shi / Zhenfeng Liu / Luca Dall'Osto / Roberto Bassi / Xinzheng Zhang / Mei Li /
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- ...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.
History
DepositionDec 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
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Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 25, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Assembly

Deposited unit
BA: Photosystem I P700 chlorophyll a apoprotein A1
BB: Photosystem I P700 chlorophyll a apoprotein A2
BC: Photosystem I iron-sulfur center
BD: Photosystem I reaction center subunit II-2, chloroplastic
BE: Photosystem I reaction center subunit IV A, chloroplastic
BF: Photosystem I reaction center subunit III, chloroplastic
BG: Photosystem I reaction center subunit V, chloroplastic
BH: Photosystem I reaction center subunit VI-2, chloroplastic
BI: Photosystem I reaction center subunit VIII
BJ: Photosystem I reaction center subunit IX
BK: Photosystem I reaction center subunit psaK, chloroplastic
BL: Photosystem I reaction center subunit XI, chloroplastic
B1: Chlorophyll a-b binding protein 6, chloroplastic
B2: Photosystem I chlorophyll a/b-binding protein 2, chloroplastic
B3: Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic
B5: Photosystem I chlorophyll a/b-binding protein 5, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)591,713221
Polymers425,12116
Non-polymers166,591205
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules BABB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 83315.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56766, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82555.883 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56767, photosystem I

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Protein , 2 types, 2 molecules BCB1

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 9049.509 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P62090, photosystem I
#13: Protein Chlorophyll a-b binding protein 6, chloroplastic / LHCI-730 / LHCII type III CAB-6 / Light-harvesting complex protein Lhca1


Mass: 26021.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q01667

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Photosystem I reaction center subunit ... , 9 types, 9 molecules BDBEBFBGBHBIBJBKBL

#4: Protein Photosystem I reaction center subunit II-2, chloroplastic / Photosystem I 20 kDa subunit 2 / PSI-D2


Mass: 22336.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SA56
#5: Protein Photosystem I reaction center subunit IV A, chloroplastic / PSI-E A


Mass: 14984.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S831
#6: Protein Photosystem I reaction center subunit III, chloroplastic / Light-harvesting complex I 17 kDa protein / PSI-F


Mass: 24203.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SHE8
#7: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 17103.271 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9S7N7
#8: Protein Photosystem I reaction center subunit VI-2, chloroplastic / PSI-H1


Mass: 15291.522 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI6
#9: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 4137.024 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56768
#10: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 5011.897 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: P56769
#11: Protein Photosystem I reaction center subunit psaK, chloroplastic / PSI-K / Photosystem I subunit X


Mass: 13219.431 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI5
#12: Protein Photosystem I reaction center subunit XI, chloroplastic / PSI-L / PSI subunit V


Mass: 23070.557 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SUI4

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Photosystem I chlorophyll a/b-binding protein ... , 3 types, 3 molecules B2B3B5

#14: Protein Photosystem I chlorophyll a/b-binding protein 2, chloroplastic / Lhca2 / LHCI type III LHCA2


Mass: 27782.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SYW8
#15: Protein Photosystem I chlorophyll a/b-binding protein 3-1, chloroplastic / Lhca3*1 / LHCI type III LHCA3


Mass: 29206.311 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9SY97
#16: Protein Photosystem I chlorophyll a/b-binding protein 5, chloroplastic / Lhca5 / LHCI type III LHCA5


Mass: 27830.961 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: Q9C639

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Sugars , 2 types, 4 molecules

#22: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#23: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 10 types, 201 molecules

#17: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 141 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#20: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H78O12S
#25: Chemical
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical
ChemComp-XAT / (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 / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H56O4 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI complex in the NDH-PSI supercomplex of Arabidopsis
Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136022 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00737149
ELECTRON MICROSCOPYf_angle_d1.5952968
ELECTRON MICROSCOPYf_dihedral_angle_d22.43411549
ELECTRON MICROSCOPYf_chiral_restr0.094570
ELECTRON MICROSCOPYf_plane_restr0.0097021

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