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- PDB-7wfg: Subcomplexes A and E in NDH complex from Arabidopsis -

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Basic information

Entry
Database: PDB / ID: 7wfg
TitleSubcomplexes A and E in NDH complex from Arabidopsis
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 7
  • NdhO
  • NdhT
KeywordsELECTRON TRANSPORT / Subcomplex A / subcomplex E / supercomplex / Arabidopsis / plant / cyclic electron transport
Function / homology
Function and homology information


NADH dehydrogenase complex (plastoquinone) assembly / NAD(P)H dehydrogenase complex (plastoquinone) / cellular response to sulfate starvation / thylakoid membrane / chloroplast thylakoid / NADPH dehydrogenase activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / chloroplast envelope / photosynthetic electron transport in photosystem I / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor ...NADH dehydrogenase complex (plastoquinone) assembly / NAD(P)H dehydrogenase complex (plastoquinone) / cellular response to sulfate starvation / thylakoid membrane / chloroplast thylakoid / NADPH dehydrogenase activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / chloroplast envelope / photosynthetic electron transport in photosystem I / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / chloroplast stroma / plastid / photosynthesis, light reaction / chloroplast thylakoid membrane / defense response to fungus / NADH dehydrogenase (ubiquinone) activity / quinone binding / photosynthesis / chloroplast / NAD binding / 4 iron, 4 sulfur cluster binding / iron ion binding / plasma membrane
Similarity search - Function
4Fe-4S dicluster domain / NAD(P)H-quinone oxidoreductase subunit O / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase, subunit N / Cyanobacterial and plastid NDH-1 subunit M / NADH dehydrogenase transmembrane subunit / NADH-quinone oxidoreductase cyanobacterial subunit N / NADH-plastoquinone oxidoreductase, subunit I ...4Fe-4S dicluster domain / NAD(P)H-quinone oxidoreductase subunit O / Cyanobacterial and plant NDH-1 subunit O / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase, subunit N / Cyanobacterial and plastid NDH-1 subunit M / NADH dehydrogenase transmembrane subunit / NADH-quinone oxidoreductase cyanobacterial subunit N / NADH-plastoquinone oxidoreductase, subunit I / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / NADH-quinone oxidoreductase, subunit D / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH dehydrogenase, subunit C / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 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
IRON/SULFUR CLUSTER / NdhO / NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / NAD(P)H-quinone oxidoreductase subunit J, chloroplastic / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H-quinone oxidoreductase subunit M, chloroplastic / NAD(P)H-quinone oxidoreductase subunit L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit N, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.33 Å
AuthorsPan, X.W. / Li, M.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2017YFA0503702 China
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China (NSFC)31770778 China
National Natural Science Foundation of China (NSFC)31930064 China
National Natural Science Foundation of China (NSFC)31970264 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
Revision 1.1Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

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Assembly

Deposited unit
H: NAD(P)H-quinone oxidoreductase subunit H, chloroplastic
I: NAD(P)H-quinone oxidoreductase subunit I, chloroplastic
J: NAD(P)H-quinone oxidoreductase subunit J, chloroplastic
K: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
L: NAD(P)H-quinone oxidoreductase subunit L, chloroplastic
M: NAD(P)H-quinone oxidoreductase subunit M, chloroplastic
N: NAD(P)H-quinone oxidoreductase subunit N, chloroplastic
O: NdhO
T: NdhT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,01012
Polymers207,9569
Non-polymers1,0553
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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NAD(P)H-quinone oxidoreductase subunit ... , 7 types, 7 molecules HIJKLMN

#1: Protein NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / NAD(P)H dehydrogenase subunit H / NADH-plastoquinone oxidoreductase 49 kDa subunit / NADH- ...NAD(P)H dehydrogenase subunit H / NADH-plastoquinone oxidoreductase 49 kDa subunit / NADH-plastoquinone oxidoreductase subunit H


Mass: 45553.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56753, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H dehydrogenase subunit I / NDH subunit I / NADH-plastoquinone oxidoreductase subunit I


Mass: 20107.314 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56755, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein NAD(P)H-quinone oxidoreductase subunit J, chloroplastic / NAD(P)H dehydrogenase subunit J / NADH-plastoquinone oxidoreductase subunit J


Mass: 18579.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56754, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#4: Protein NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H dehydrogenase subunit K / NADH-plastoquinone oxidoreductase subunit K


Mass: 25396.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: P56756, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein NAD(P)H-quinone oxidoreductase subunit L, chloroplastic / NAD(P)H dehydrogenase subunit L / NDH subunit L / NDH-L / NADH-plastoquinone oxidoreductase subunit ...NAD(P)H dehydrogenase subunit L / NDH subunit L / NDH-L / NADH-plastoquinone oxidoreductase subunit L / Protein CHLORORESPIRATORY REDUCTION 23


Mass: 21987.850 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9CAC5, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NAD(P)H-quinone oxidoreductase subunit M, chloroplastic / NAD(P)H dehydrogenase subunit M / NDH subunit M / NDH-M / NADH-plastoquinone oxidoreductase subunit M


Mass: 24820.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q2V2S7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#7: Protein NAD(P)H-quinone oxidoreductase subunit N, chloroplastic / NAD(P)H dehydrogenase subunit N / NDH subunit N / NDH-N / NADH-plastoquinone oxidoreductase subunit N


Mass: 23430.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress)
References: UniProt: Q9LVM2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions

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Protein , 2 types, 2 molecules OT

#8: Protein NdhO


Mass: 17679.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / References: UniProt: A0A178WB24
#9: Protein NdhT


Mass: 10400.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: All Residues in NdhT were modeled as UNK. The real sequence of the entity is: ...Details: All Residues in NdhT were modeled as UNK. The real sequence of the entity is: MAYATSTYARTSCIILPKIQNGAHFTDNTKAFRRITARRVTRISSQGPTKPPKPSPGVDTRIHWESPDEGWIGGRSDPAKSVDEDKTNLLSDEKFAELIKDSFDSHYQFLGVSTDAHLEEIKSAYRRLSKEYHPDTTSLPLKTASEKFMKLREVYNVLSDEETRRFYDWTLAQEVASRQAEKMRMKLEDPKEQDFRGYESIPDMVDRLGGRNMELSDQAMTALTFDILIVLFAVCCIVFVIVFKDPSY
Source: (natural) Arabidopsis thaliana (thale cress)

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Non-polymers , 1 types, 3 molecules

#10: 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

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Details

Has ligand of interestY

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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: Subcomplex A and E in NDH complex from Arabidopsis / Type: COMPLEX / Entity ID: #1-#9 / 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 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76085 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00510017
ELECTRON MICROSCOPYf_angle_d0.93613606
ELECTRON MICROSCOPYf_dihedral_angle_d17.0973475
ELECTRON MICROSCOPYf_chiral_restr0.0571564
ELECTRON MICROSCOPYf_plane_restr0.0071735

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