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- PDB-7eu3: Chloroplast NDH complex -

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Basic information

Entry
Database: PDB / ID: 7eu3
TitleChloroplast NDH complex
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 13
  • (Photosynthetic NDH subunit of subcomplex ...) x 10
  • NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
  • Unidentified stromal protein
KeywordsPHOTOSYNTHESIS / chloroplast NAD(P)H-quinone oxidoreductase / cyclic electron transport
Function / homology
Function and homology information


Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / chloroplast thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase complex / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / NADH dehydrogenase activity / chloroplast thylakoid membrane / photosynthesis, light reaction / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / aerobic respiration / mitochondrial membrane / NAD binding / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
: / NADH-quinone oxidoreductase chain 4 / NADH-plastoquinone oxidoreductase, subunit I / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / Rossmann fold - #12280 / Helix Hairpins - #3510 / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 ...: / NADH-quinone oxidoreductase chain 4 / NADH-plastoquinone oxidoreductase, subunit I / NAD(P)H-quinone oxidoreductase subunit 2, N-terminal / NAD(P)H-quinone oxidoreductase subunit 2 N-terminal / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / Rossmann fold - #12280 / Helix Hairpins - #3510 / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / Chitinase A; domain 3 - #40 / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Chitinase A; domain 3 / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NADH-quinone oxidoreductase, chain I / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / 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:ubiquinone oxidoreductase / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:quinone oxidoreductase/Mrp antiporter, TM / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / 4Fe-4S dicluster domain / 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 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Helix Hairpins / Roll / Up-down Bundle / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-CAROTENE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / IRON/SULFUR CLUSTER / Chem-SQD / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit K, chloroplastic ...BETA-CAROTENE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / IRON/SULFUR CLUSTER / Chem-SQD / NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NAD(P)H-quinone oxidoreductase subunit H, chloroplastic / NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
Similarity search - Component
Biological speciesHordeum vulgare (barley)
Hordeum vulgare subsp. spontaneum (wild barley)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, W.D. / Shen, L. / Tang, K. / Han, G.Y. / Zhang, X. / Shen, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
CitationJournal: Nature / Year: 2022
Title: Architecture of the chloroplast PSI-NDH supercomplex in Hordeum vulgare.
Authors: Liangliang Shen / Kailu Tang / Wenda Wang / Chen Wang / Hangjun Wu / Zhiyuan Mao / Shaoya An / Shenghai Chang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Xing Zhang /
Abstract: The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex ...The chloroplast NADH dehydrogenase-like (NDH) complex is composed of at least 29 subunits and has an important role in mediating photosystem I (PSI) cyclic electron transport (CET). The NDH complex associates with PSI to form the PSI-NDH supercomplex and fulfil its function. Here, we report cryo-electron microscopy structures of a PSI-NDH supercomplex from barley (Hordeum vulgare). The structures reveal that PSI-NDH is composed of two copies of the PSI-light-harvesting complex I (LHCI) subcomplex and one NDH complex. Two monomeric LHCI proteins, Lhca5 and Lhca6, mediate the binding of two PSI complexes to NDH. Ten plant chloroplast-specific NDH subunits are presented and their exact positions as well as their interactions with other subunits in NDH are elucidated. In all, this study provides a structural basis for further investigations on the functions and regulation of PSI-NDH-dependent CET.
History
DepositionMay 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 6, 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

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Assembly

Deposited unit
A: NAD(P)H-quinone oxidoreductase subunit 1, chloroplastic
B: NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic
C: NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic
D: NAD(P)H-quinone oxidoreductase chain 4, chloroplastic
E: NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic
F: NAD(P)H-quinone oxidoreductase subunit F
G: NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic
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
K: NAD(P)H-quinone oxidoreductase subunit K, chloroplastic
L: NAD(P)H-quinone oxidoreductase subunit L
M: NAD(P)H-quinone oxidoreductase subunit M
N: NAD(P)H-quinone oxidoreductase subunit N
T: Unidentified stromal protein
1: Photosynthetic NDH subunit of subcomplex L1
2: Photosynthetic NDH subunit of subcomplex L2
3: Photosynthetic NDH subunit of subcomplex L3
4: Photosynthetic NDH subunit of subcomplex L4
5: Photosynthetic NDH subunit of subcomplex L5
6: Photosynthetic NDH subunit of subcomplex B1
7: Photosynthetic NDH subunit of subcomplex B2
8: Photosynthetic NDH subunit of subcomplex B3
9: Photosynthetic NDH subunit of subcomplex B4
0: Photosynthetic NDH subunit of subcomplex B5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)707,88630
Polymers704,68525
Non-polymers3,2025
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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NAD(P)H-quinone oxidoreductase subunit ... , 13 types, 13 molecules ABCEFGHIJKLMN

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


Mass: 38544.336 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley)
References: UniProt: P92432, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#2: Protein NAD(P)H-quinone oxidoreductase subunit 2, chloroplastic / NAD(P)H dehydrogenase / subunit 2 / NADH-plastoquinone oxidoreductase subunit 2


Mass: 53452.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z268, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#3: Protein NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3


Mass: 13299.608 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z1L1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#5: Protein NAD(P)H-quinone oxidoreductase subunit 4L, chloroplastic / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L


Mass: 11199.190 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley)
References: UniProt: A0A218LNA9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#6: Protein NAD(P)H-quinone oxidoreductase subunit F


Mass: 87552.930 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#7: Protein NAD(P)H-quinone oxidoreductase subunit 6, chloroplastic


Mass: 19587.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: A0A4Y5SEJ9, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#8: 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: 44563.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z272, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#9: Protein NAD(P)H-quinone oxidoreductase subunit I, chloroplastic / NAD(P)H dehydrogenase subunit I / NDH subunit I / NADH-plastoquinone oxidoreductase subunit I


Mass: 19271.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley)
References: UniProt: A0A218LNN1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#10: Protein NAD(P)H-quinone oxidoreductase subunit J


Mass: 18733.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#11: Protein NAD(P)H-quinone oxidoreductase subunit K, chloroplastic / NAD(P)H dehydrogenase subunit K / NADH-plastoquinone oxidoreductase subunit K


Mass: 27568.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z232, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#12: Protein NAD(P)H-quinone oxidoreductase subunit L


Mass: 22240.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#13: Protein NAD(P)H-quinone oxidoreductase subunit M


Mass: 24051.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#14: Protein NAD(P)H-quinone oxidoreductase subunit N


Mass: 25928.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)

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Protein , 2 types, 2 molecules DT

#4: Protein NAD(P)H-quinone oxidoreductase chain 4, chloroplastic / NAD(P)H dehydrogenase / chain 4 / NADH-plastoquinone oxidoreductase chain 4


Mass: 56222.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
References: UniProt: S4Z8N2, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions
#15: Protein Unidentified stromal protein


Mass: 5209.413 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)

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Photosynthetic NDH subunit of subcomplex ... , 10 types, 10 molecules 1234567890

#16: Protein Photosynthetic NDH subunit of subcomplex L1


Mass: 17835.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#17: Protein Photosynthetic NDH subunit of subcomplex L2


Mass: 23946.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#18: Protein Photosynthetic NDH subunit of subcomplex L3


Mass: 24733.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#19: Protein Photosynthetic NDH subunit of subcomplex L4


Mass: 13954.360 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#20: Protein Photosynthetic NDH subunit of subcomplex L5


Mass: 25818.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#21: Protein Photosynthetic NDH subunit of subcomplex B1


Mass: 51675.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#22: Protein Photosynthetic NDH subunit of subcomplex B2


Mass: 38079.977 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#23: Protein Photosynthetic NDH subunit of subcomplex B3


Mass: 13313.331 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#24: Protein Photosynthetic NDH subunit of subcomplex B4


Mass: 9756.810 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)
#25: Protein Photosynthetic NDH subunit of subcomplex B5


Mass: 18146.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Hordeum vulgare subsp. spontaneum (wild barley)

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Non-polymers , 4 types, 5 molecules

#26: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#27: Chemical ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#28: 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.: 2 / Source method: obtained synthetically / Formula: C41H78O12S
#29: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4

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Details

Has ligand of interestN
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: Chloroplast NDH complex of Barley / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL
Source (natural)Organism: Hordeum vulgare subsp. spontaneum (wild barley)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 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:phenix.real_space_refine) / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103844 / Symmetry type: POINT
RefinementCross valid method: THROUGHOUT
Displacement parametersBiso max: 346.78 Å2 / Biso mean: 138.3381 Å2 / Biso min: 30 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00342856
ELECTRON MICROSCOPYf_angle_d0.73658287
ELECTRON MICROSCOPYf_chiral_restr0.0456609
ELECTRON MICROSCOPYf_plane_restr0.0057340
ELECTRON MICROSCOPYf_dihedral_angle_d26.616003

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