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- EMDB-9989: Supercomplex for cylic electron transport in cyanobacteria -

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Basic information

Entry
Database: EMDB / ID: EMD-9989
TitleSupercomplex for cylic electron transport in cyanobacteria
Map data
SampleElectron transport complex NDH-Fd from cyanobacteria
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 12
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • NADH dehydrogenase subunit 5
  • NADH-quinone oxidoreductase subunit JNADH dehydrogenase (quinone)
  • (proton-translocating NADH-quinone dehydrogenase subunit ...) x 2
  • Tlr0636 protein
  • Tlr0472 protein
  • Ferredoxin-1
  • (ligand) x 7
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 / 2 iron, 2 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 / 2 iron, 2 sulfur cluster binding / NAD binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / iron ion binding / integral component of membrane / plasma membrane / metal ion binding
4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH dehydrogenase, subunit C / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH:ubiquinone oxidoreductase / NADH-plastoquinone oxidoreductase, chain 5 / NADH-plastoquinone oxidoreductase, subunit I / 2Fe-2S ferredoxin, iron-sulphur binding site / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH-ubiquinone oxidoreductase, 20 Kd subunit / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 ...4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH dehydrogenase, subunit C / NADH:ubiquinone/plastoquinone oxidoreductase, chloroplast chain 5, C-terminal / NADH:ubiquinone oxidoreductase / NADH-plastoquinone oxidoreductase, chain 5 / NADH-plastoquinone oxidoreductase, subunit I / 2Fe-2S ferredoxin, iron-sulphur binding site / 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:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH-quinone oxidoreductase, chain M/4 / Ferredoxin [2Fe-2S], plant / Beta-grasp domain superfamily / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH:ubiquinone oxidoreductase, 30kDa subunit, conserved site / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / NADH:ubiquinone oxidoreductase, subunit 1, conserved site / NADH-plastoquinone oxidoreductase, chain 5 subgroup / NADH:quinone oxidoreductase/Mrp antiporter, membrane subunit / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminal / NAD(P)H-quinone oxidoreductase subunit L / 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 / 2Fe-2S ferredoxin-like superfamily / [NiFe]-hydrogenase, large subunit / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NAD(P)H-quinone oxidoreductase subunit D/H / NADH:ubiquinone/plastoquinone oxidoreductase, chain 6 / NADH dehydrogenase-like complex, subunit S / Protein of unknown function DUF2996 / NAD(P)H-quinone oxidoreductase subunit O / NAD(P)H-quinone oxidoreductase, subunit N / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / 2Fe-2S ferredoxin-type iron-sulfur binding domain / NADH-ubiquinone oxidoreductase chain 4L/K / NADH-quinone oxidoreductase, subunit D / NADH:ubiquinone oxidoreductase, 30kDa subunit / NAD(P)H-quinone oxidoreductase subunit M
NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit M / Tlr0472 protein / 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 J / NAD(P)H-quinone oxidoreductase subunit K ...NAD(P)H-quinone oxidoreductase subunit 4L / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit M / Tlr0472 protein / 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 J / 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 H / NAD(P)H-quinone oxidoreductase subunit 3 / Ferredoxin-1 / NAD(P)H-quinone oxidoreductase subunit O
Biological speciesThermosynechococcus elongatus BP-1 (Cyanobacteria) / Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsPan X / Cao D / Xie F / Zhang Z / Li M
Funding support China, 9 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0503702 China
Ministry of Science and Technology (China)2016YFA0502900 China
Ministry of Science and Technology (China)2017YFA0504700 China
Chinese Academy of SciencesXDB08030204 China
Chinese Academy of SciencesXDB08020302 China
Chinese Academy of SciencesQYZDB-SSW-SMC005 China
Chinese Academy of SciencesXDB27020106 China
National Natural Science Foundation of China31600609 China
National Natural Science Foundation of China31770778 China
Citation
Journal: Nat Commun / Year: 2020
Title: Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase.
Authors: Xiaowei Pan / Duanfang Cao / Fen Xie / Fang Xu / Xiaodong Su / Hualing Mi / Xinzheng Zhang / Mei Li /
Abstract: NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron ...NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron transport from ferredoxin (Fd) to plastoquinone (PQ) and proton pumping from cytoplasm to the lumen that drives the ATP production. NDH-1L-dependent CEF increases the ATP/NADPH ratio, and is therefore pivotal for oxygenic phototrophs to function under stress. Here we report two structures of NDH-1L from Thermosynechococcus elongatus BP-1, in complex with one Fd and an endogenous PQ, respectively. Our structures represent the complete model of cyanobacterial NDH-1L, revealing the binding manner of NDH-1L with Fd and PQ, as well as the structural elements crucial for proper functioning of the NDH-1L complex. Together, our data provides deep insights into the electron transport from Fd to PQ, and its coupling with proton translocation in NDH-1L.
#1: Journal: To Be Published
Title: Structure of photosystem from green alga.
Authors: Su X / Ma J / Pan X / Zhao X / Chang W / Liu Z / Zhang X / Li M
Validation ReportPDB-ID: 6khi

SummaryFull reportAbout validation report
History
DepositionJul 15, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6khi
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9989.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 416. Å
1.04 Å/pix.
x 400 pix.
= 416. Å
1.04 Å/pix.
x 400 pix.
= 416. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.11657772 - 0.41748697
Average (Standard dev.)0.00034288695 (±0.0069694603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-200-200-200
Dimensions400400400
Spacing400400400
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z416.000416.000416.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS-200-200-200
NC/NR/NS400400400
D min/max/mean-0.1170.4170.000

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Supplemental data

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Sample components

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Entire Electron transport complex NDH-Fd from cyanobacteria

EntireName: Electron transport complex NDH-Fd from cyanobacteria / Number of components: 28

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Component #1: protein, Electron transport complex NDH-Fd from cyanobacteria

ProteinName: Electron transport complex NDH-Fd from cyanobacteria / Recombinant expression: No
SourceSpecies: Thermosynechococcus elongatus 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) / Strain: BP-1

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Component #3: 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) / Strain: BP-1

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Component #4: 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) / Strain: BP-1

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Component #5: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #6: 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) / Strain: BP-1

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Component #7: 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) / Strain: BP-1

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Component #8: protein, NADH-quinone oxidoreductase subunit J

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

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Component #9: 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) / Strain: BP-1

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Component #10: 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) / Strain: BP-1

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Component #11: 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) / Strain: BP-1

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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) / Strain: BP-1

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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) / Strain: BP-1

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Component #14: 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) / Strain: BP-1

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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) / Strain: BP-1

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Component #16: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #17: protein, proton-translocating NADH-quinone dehydrogenase subunit P

ProteinName: proton-translocating NADH-quinone dehydrogenase subunit P
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.878649 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria) / Strain: BP-1

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Component #18: protein, proton-translocating NADH-quinone dehydrogenase subunit Q

ProteinName: proton-translocating NADH-quinone dehydrogenase subunit Q
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.858724 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria) / Strain: BP-1

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Component #19: protein, Tlr0636 protein

ProteinName: Tlr0636 protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.462559 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria) / Strain: BP-1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #20: protein, Tlr0472 protein

ProteinName: Tlr0472 protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.016489 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria) / Strain: BP-1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #21: protein, Ferredoxin-1

ProteinName: Ferredoxin-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.853959 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria) / Strain: BP-1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #22: ligand, DIGALACTOSYL DIACYL GLYCEROL (DGDG)

LigandName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.949299 kDa

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Component #23: ligand, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

LigandName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.72297 kDa

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Component #24: ligand, 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL...

LigandName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.795116 kDa

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Component #25: ligand, BETA-CAROTENE

LigandName: BETA-CAROTENE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.536873 kDa

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Component #26: ligand, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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

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Component #27: 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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Component #28: ligand, FE2/S2 (INORGANIC) CLUSTER

LigandName: FE2/S2 (INORGANIC) CLUSTER / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.17582 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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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: 60 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: 152003
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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