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Entry
Database: PDB / ID: 6hum
TitleStructure of the photosynthetic complex I from Thermosynechococcus elongatus
Components
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 12
  • (NADH dehydrogenase subunit ...) x 2
  • (Proton-translocating NADH-quinone dehydrogenase subunit ...) x 2
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • Tlr0636 protein
KeywordsPROTON TRANSPORT / Respiratory Complex / Ferredoxin / Cyclic electron flow / Complex I / Membrane protein complex
Function / homology
Function and homology information


Translocases; Catalysing the translocation of hydrons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / NADH dehydrogenase (ubiquinone) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ATP synthesis coupled electron transport / thylakoid membrane / photosynthesis, light reaction / quinone binding / 4 iron, 4 sulfur cluster binding / NAD binding ...Translocases; Catalysing the translocation of hydrons; Linked to oxidoreductase reactions / photosynthetic electron transport chain / NADH dehydrogenase (ubiquinone) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ATP synthesis coupled electron transport / thylakoid membrane / photosynthesis, light reaction / quinone binding / 4 iron, 4 sulfur cluster binding / NAD binding / iron ion binding / integral component of membrane / plasma membrane
NADH-quinone oxidoreductase, subunit D superfamily / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site ...NADH-quinone oxidoreductase, subunit D superfamily / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit L / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NAD(P)H-quinone oxidoreductase, subunit N / NAD(P)H-quinone oxidoreductase subunit O / NADH dehydrogenase-like complex, subunit S / NADH-quinone oxidoreductase chain 4 / NADH-quinone oxidoreductase, chain I / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / [NiFe]-hydrogenase, large subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-quinone oxidoreductase, chain M/4 / NADH dehydrogenase, subunit C / NADH dehydrogenase / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NAD(P)H dehydrogenase subunit S / Cyanobacterial and plant NDH-1 subunit O / NADH-quinone oxidoreductase cyanobacterial subunit N / Cyanobacterial and plastid NDH-1 subunit M / NADH dehydrogenase transmembrane subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / 4Fe-4S dicluster domain / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, 30kDa subunit / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH:ubiquinone oxidoreductase / NADH-plastoquinone oxidoreductase, chain 5 / NADH-plastoquinone oxidoreductase, subunit I / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / Proton-conducting membrane transporter / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / Helix Hairpins - #3510 / SH3 type barrels. - #140 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Helix Hairpins / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H-quinone oxidoreductase subunit 4L / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit N / NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H-quinone oxidoreductase subunit H / Tlr0636 protein / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit O ...NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H-quinone oxidoreductase subunit 4L / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit N / NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H-quinone oxidoreductase subunit H / Tlr0636 protein / NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit O / NAD(P)H-quinone oxidoreductase chain 4 1 / NAD(P)H-quinone oxidoreductase subunit K / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H-quinone oxidoreductase subunit L
Biological speciesThermosynechococcus elongatus BP-1 (Cyanobacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsSchuller, J.M. / Schuller, S.K. / Kurisu, G. / Engel, B.D. / Nowaczyk, M.M.
Funding support Germany, Japan, Australia, 7items
OrganizationGrant numberCountry
German Research FoundationFOR2092 Germany
German Research FoundationNO 836/1-1 Germany
Max Planck Society Germany
German Federal Ministry for Education and ResearchRESOLV Germany
International Joint Research Promotion Program Japan
Japan Science and TechnologyJPMJCR13M4 Japan
FT140100834 Australia
CitationJournal: Science / Year: 2019
Title: Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer.
Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa ...Authors: Jan M Schuller / James A Birrell / Hideaki Tanaka / Tsuyoshi Konuma / Hannes Wulfhorst / Nicholas Cox / Sandra K Schuller / Jacqueline Thiemann / Wolfgang Lubitz / Pierre Sétif / Takahisa Ikegami / Benjamin D Engel / Genji Kurisu / Marc M Nowaczyk /
Abstract: Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy ...Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of photosynthetic complex I from the cyanobacterium The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: em_admin / pdbx_data_processing_status ...em_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _em_admin.last_update
Revision 1.2Jan 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Assembly

Deposited unit
A: NAD(P)H-quinone oxidoreductase subunit 1
C: NAD(P)H-quinone oxidoreductase subunit 3
D: NAD(P)H-quinone oxidoreductase chain 4 1
E: NAD(P)H-quinone oxidoreductase subunit 4L
B: NAD(P)H-quinone oxidoreductase subunit 2
G: NADH dehydrogenase subunit 6
J: NAD(P)H-quinone oxidoreductase subunit J
P: Proton-translocating NADH-quinone dehydrogenase subunit P NdhP
H: NAD(P)H-quinone oxidoreductase subunit H
I: NAD(P)H-quinone oxidoreductase subunit I
K: NAD(P)H-quinone oxidoreductase subunit K
L: NAD(P)H-quinone oxidoreductase subunit L
F: NADH dehydrogenase subunit 5
N: NAD(P)H-quinone oxidoreductase subunit N
M: NAD(P)H-quinone oxidoreductase subunit M
S: Tlr0636 protein
O: NAD(P)H-quinone oxidoreductase subunit O
Q: Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,56023
Polymers453,18118
Non-polymers2,3795
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area96820 Å2
ΔGint-765 kcal/mol
Surface area118600 Å2
MethodPISA

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Components

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NAD(P)H-quinone oxidoreductase subunit ... , 12 types, 12 molecules ACEBJHIKLNMO

#1: Protein NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H dehydrogenase I subunit 1 / NDH-1 subunit 1 / NDH-A


Mass: 40565.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL32, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Protein NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H dehydrogenase subunit 3 / NADH-plastoquinone oxidoreductase subunit 3 / NDH-1 subunit 3 / NDH-C


Mass: 15013.919 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJ02, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#4: Protein NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H dehydrogenase subunit 4L / NADH-plastoquinone oxidoreductase subunit 4L / NDH-1 / subunit 4L / NDH-E


Mass: 11140.265 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL29, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#5: Protein NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H dehydrogenase subunit 2 / NADH-plastoquinone oxidoreductase subunit 2 / NDH-1 / subunit 2


Mass: 55168.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DMR6, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#7: Protein NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H dehydrogenase subunit J / NADH-plastoquinone oxidoreductase subunit J / NDH-1 subunit J / NDH-J


Mass: 19363.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJ01, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#9: Protein NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H dehydrogenase subunit H / NADH-plastoquinone oxidoreductase subunit H / NDH-1 subunit H / NDH-H


Mass: 45271.184 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJD9, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#10: Protein NAD(P)H-quinone oxidoreductase subunit I / NAD(P)H dehydrogenase I subunit I / NDH-1 subunit I / NDH-I


Mass: 22444.801 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL31, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#11: Protein NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H dehydrogenase I subunit K / NDH-1 subunit K / NDH-K


Mass: 25766.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKZ4, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#12: Protein NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H dehydrogenase I subunit L / NDH-1 subunit L / NDH-L


Mass: 8575.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKZ3, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#14: Protein NAD(P)H-quinone oxidoreductase subunit N / NAD(P)H dehydrogenase I subunit N / NDH-N


Mass: 16656.182 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DJU2, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#15: Protein NAD(P)H-quinone oxidoreductase subunit M / NAD(P)H dehydrogenase I subunit M / NDH-M


Mass: 12584.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DLN5, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#17: Protein NAD(P)H-quinone oxidoreductase subunit O / NAD(P)H dehydrogenase I subunit O / NDH-1 subunit O / NDH-O


Mass: 7877.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DMU4, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor

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Protein , 2 types, 2 molecules DS

#3: Protein NAD(P)H-quinone oxidoreductase chain 4 1 / NAD(P)H dehydrogenase I / chain 4 1 / NDH-1


Mass: 57847.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKY0, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#16: Protein Tlr0636 protein


Mass: 12462.559 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL61

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NADH dehydrogenase subunit ... , 2 types, 2 molecules GF

#6: Protein NADH dehydrogenase subunit 6 /


Mass: 21580.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DL30
#13: Protein NADH dehydrogenase subunit 5 /


Mass: 72025.352 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
References: UniProt: Q8DKX9

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Proton-translocating NADH-quinone dehydrogenase subunit ... , 2 types, 2 molecules PQ

#8: Protein/peptide Proton-translocating NADH-quinone dehydrogenase subunit P NdhP


Mass: 4630.392 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)
#18: Protein/peptide Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ


Mass: 4206.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Non-polymers , 3 types, 5 molecules

#19: Chemical ChemComp-BCR / BETA-CAROTENE / Beta-Carotene


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#20: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H86O10
#21: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4

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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: photosynthetic complex I / Type: COMPLEX / Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18 / Source: NATURAL
Source (natural)Organism: Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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 FIELDBright-field microscopy
Image recordingElectron dose: 49.93 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 133485 / Symmetry type: POINT

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