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- EMDB-0281: Structure of the photosynthetic complex I from Thermosynechococcu... -

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Basic information

Entry
Database: EMDB / ID: EMD-0281
TitleStructure of the photosynthetic complex I from Thermosynechococcus elongatus
Map data
Samplephotosynthetic complex I
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 12
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • (NADH dehydrogenase subunit ...) x 2
  • (Proton-translocating NADH-quinone dehydrogenase subunit ...) x 2
  • Tlr0636 protein
  • (ligand) x 3
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 / NAD binding / 4 iron, 4 sulfur cluster 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 / NAD binding / 4 iron, 4 sulfur cluster binding / iron ion binding / integral component of membrane / plasma membrane
4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH dehydrogenase, subunit C / 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 / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-quinone oxidoreductase, chain I / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit ...4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH dehydrogenase, subunit C / 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 / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH-quinone oxidoreductase, chain I / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH-quinone oxidoreductase, chain M/4 / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NAD(P)H-quinone oxidoreductase, subunit N / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NAD(P)H-quinone oxidoreductase subunit M / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / NADH-quinone oxidoreductase chain 4 / NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / [NiFe]-hydrogenase, large subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NADH dehydrogenase-like complex, subunit S / NAD(P)H-quinone oxidoreductase subunit O / 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 / NAD(P)H-quinone oxidoreductase subunit L
NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit M / Tlr0636 protein / NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit L ...NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit M / Tlr0636 protein / NAD(P)H-quinone oxidoreductase subunit 1 / NAD(P)H-quinone oxidoreductase subunit I / NADH-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit K / NAD(P)H-quinone oxidoreductase subunit L / NAD(P)H-quinone oxidoreductase chain 4 1 / NADH dehydrogenase subunit 5 / NAD(P)H-quinone oxidoreductase subunit N / NAD(P)H-quinone oxidoreductase subunit 3 / NAD(P)H-quinone oxidoreductase subunit J / NAD(P)H-quinone oxidoreductase subunit O
Biological speciesThermosynechococcus elongatus (strain BP-1) (Cyanobacteria) / Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsSchuller JM / Schuller SK / Kurisu G / Engel BD / Nowaczyk MM
Funding support Germany, Japan, 5 items
OrganizationGrant numberCountry
German Research FoundationFOR2092 Germany
Max Planck Society Germany
German Research FoundationNO 836/1-1 Germany
German Federal Ministry for Education and ResearchRESOLV Germany
Japan Science and TechnologyJPMJCR13M4 Japan
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 ReportPDB-ID: 6hum

SummaryFull reportAbout validation report
History
DepositionOct 9, 2018-
Header (metadata) releaseJan 9, 2019-
Map releaseJan 9, 2019-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hum
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6hum
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0281.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 300 pix.
= 405. Å
1.35 Å/pix.
x 300 pix.
= 405. Å
1.35 Å/pix.
x 300 pix.
= 405. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.22975716 - 0.65928394
Average (Standard dev.)0.0000946623 (±0.0068258634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z405.000405.000405.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2300.6590.000

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Supplemental data

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Sample components

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Entire photosynthetic complex I

EntireName: photosynthetic complex I / Number of components: 22

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Component #1: protein, photosynthetic complex I

ProteinName: photosynthetic complex I / Recombinant expression: No
SourceSpecies: Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)

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Component #2: protein, NAD(P)H-quinone oxidoreductase subunit 1

ProteinName: NAD(P)H-quinone oxidoreductase subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.565984 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #3: protein, NAD(P)H-quinone oxidoreductase subunit 3

ProteinName: NAD(P)H-quinone oxidoreductase subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.013919 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #4: protein, NAD(P)H-quinone oxidoreductase chain 4 1

ProteinName: NAD(P)H-quinone oxidoreductase chain 4 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 57.847504 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #5: protein, NAD(P)H-quinone oxidoreductase subunit 4L

ProteinName: NAD(P)H-quinone oxidoreductase subunit 4L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 11.140265 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #6: protein, NAD(P)H-quinone oxidoreductase subunit 2

ProteinName: NAD(P)H-quinone oxidoreductase subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.168543 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #7: protein, NADH dehydrogenase subunit 6

ProteinName: NADH dehydrogenase subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.580568 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #8: protein, NAD(P)H-quinone oxidoreductase subunit J

ProteinName: NAD(P)H-quinone oxidoreductase subunit J / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.363789 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #9: protein, Proton-translocating NADH-quinone dehydrogenase subunit ...

ProteinName: Proton-translocating NADH-quinone dehydrogenase subunit P NdhP
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.630392 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #10: protein, NAD(P)H-quinone oxidoreductase subunit H

ProteinName: NAD(P)H-quinone oxidoreductase subunit H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.271184 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #11: protein, NAD(P)H-quinone oxidoreductase subunit I

ProteinName: NAD(P)H-quinone oxidoreductase subunit I / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.444801 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #12: protein, NAD(P)H-quinone oxidoreductase subunit K

ProteinName: NAD(P)H-quinone oxidoreductase subunit K / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.766998 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #13: protein, NAD(P)H-quinone oxidoreductase subunit L

ProteinName: NAD(P)H-quinone oxidoreductase subunit L / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.575137 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #14: protein, NADH dehydrogenase subunit 5

ProteinName: NADH dehydrogenase subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.025352 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #15: protein, NAD(P)H-quinone oxidoreductase subunit N

ProteinName: NAD(P)H-quinone oxidoreductase subunit N / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.656182 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #16: protein, NAD(P)H-quinone oxidoreductase subunit M

ProteinName: NAD(P)H-quinone oxidoreductase subunit M / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.584056 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #17: protein, Tlr0636 protein

ProteinName: Tlr0636 protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.462559 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #18: protein, NAD(P)H-quinone oxidoreductase subunit O

ProteinName: NAD(P)H-quinone oxidoreductase subunit O / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.877076 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #19: protein, Proton-translocating NADH-quinone dehydrogenase subunit ...

ProteinName: Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.206993 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #20: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #21: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

LigandName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.787158 kDa

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Component #22: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: OTHER

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 49.93 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 133485
3D reconstructionResolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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