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- EMDB-0415: T.elongatus NDH (data-set 1) -

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Entry
Database: EMDB / ID: 0415
TitleT.elongatus NDH (data-set 1)
Map dataCalibrated voxel size of 1.068
SampleNAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L) from T.elongatus
  • (NAD(P)H-quinone oxidoreductase subunit ...) x 11
  • Tlr0636 protein
  • NdhA
  • Proton-translocating NADH-quinone dehydrogenase subunit P NdhP
  • NADH dehydrogenase subunit 5
  • NAD(P)H-quinone oxidoreductase chain 4 1
  • NADH-quinone oxidoreductase subunit JNADH dehydrogenase (quinone)
  • ligand
Function / homology[NiFe]-hydrogenase, large subunit / NADH dehydrogenase transmembrane subunit / 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 ...[NiFe]-hydrogenase, large subunit / NADH dehydrogenase transmembrane subunit / 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 / NAD(P)H-quinone oxidoreductase subunit D/H / NADH-quinone oxidoreductase chain 4 / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site / NADH-quinone oxidoreductase, subunit D superfamily / NADH:ubiquinone oxidoreductase, subunit 3 superfamily / NADH-ubiquinone oxidoreductase chain 4L/Mnh complex subunit C1-like / NADH dehydrogenase / Respiratory-chain NADH dehydrogenase, 30 Kd subunit / Respiratory-chain NADH dehydrogenase, 49 Kd subunit / Proton-conducting membrane transporter / NADH-ubiquinone/plastoquinone oxidoreductase chain 4L / NADH-ubiquinone/plastoquinone oxidoreductase chain 6 / NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / NADH-quinone oxidoreductase, chain M/4 / Cyanobacterial and plastid NDH-1 subunit M / NADH-ubiquinone oxidoreductase chain 4L/K / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / Respiratory-chain NADH dehydrogenase 20 Kd subunit signature. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory chain NADH dehydrogenase 30 Kd subunit signature. / Respiratory chain NADH dehydrogenase 49 Kd subunit signature. / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S dicluster domain / Cyanobacterial and plant NDH-1 subunit O / NADH-quinone oxidoreductase cyanobacterial subunit N / NAD(P)H dehydrogenase subunit S / NADH:ubiquinone/plastoquinone oxidoreductase, chain 3 / NADH-quinone oxidoreductase, subunit D / NADH-quinone oxidoreductase, chain I / 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 / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, 20 Kd subunit / Translocases, Catalysing the translocation of hydrons, Linked to oxidoreductase reactions / NADH dehydrogenase (ubiquinone) activity / photosynthetic electron transport chain / ATP synthesis coupled electron transport / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / 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 J / NAD(P)H-quinone oxidoreductase subunit O / 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 / NAD(P)H-quinone oxidoreductase subunit H / NAD(P)H-quinone oxidoreductase subunit 4L / 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 / Proton-translocating NADH-quinone dehydrogenase subunit P NdhP
Function and homology information
SourceThermosynechococcus elongatus BP-1 (Cyanobacteria) / Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsLaughlin TG / Bayne A / Trempe J-F / Savage DF / Davies KM
CitationJournal: Nature / Year: 2019
Title: Structure of the complex I-like molecule NDH of oxygenic photosynthesis.
Authors: Thomas G Laughlin / Andrew N Bayne / Jean-François Trempe / David F Savage / Karen M Davies
Validation ReportPDB-ID: 6nbq

SummaryFull report
PDB-ID: 6nby

SummaryFull report
About validation report
DateDeposition: Dec 9, 2018 / Header (metadata) release: Dec 19, 2018 / Map release: Feb 27, 2019 / Last update: Mar 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nbq
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6nby
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0415.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.07 Å/pix.
= 384.48 Å
360 pix
1.07 Å/pix.
= 384.48 Å
360 pix
1.07 Å/pix.
= 384.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.13177162 - 0.32366726
Average (Standard dev.)-0.0000007916531 (0.007401498)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0681.0681.068
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z384.480384.480384.480
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1320.324-0.000

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Supplemental data

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Mask #1

Fileemd_0415_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L) from T.elo...

EntireName: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L) from T.elongatus
Details: NdhQ not observed in density / Number of components: 19

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Component #1: protein, NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L) f...

ProteinName: NAD(P)H dehydrogenase-like complex (NDH/NDH-1_1/NDH1L) from T.elongatus
Details: NdhQ not observed in density / Recombinant expression: No
MassExperimental: 400 kDa
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Component #2: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #3: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #4: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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

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Component #6: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #7: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #8: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #9: 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 #10: protein, Tlr0636 protein

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

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Component #11: protein, NdhA

ProteinName: NdhA / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.15773 kDa
SourceSpecies: Thermosynechococcus elongatus (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #12: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #13: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #14: protein, Proton-translocating NADH-quinone dehydrogenase subunit ...

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

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Component #15: protein, NADH dehydrogenase subunit 5

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

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Component #16: 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 #17: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #18: 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 (strain BP-1) (Cyanobacteria)
Strain: BP-1

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Component #19: 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 solutionSpecimen conc.: 0.01 mg/ml / pH: 6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: incubate on grid for 30 seconds and blot 2.5 seconds before plunging.

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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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2519 / Details: One image per hole, focusing at each image.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 81670
Details: Super-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size.
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Corelation coefficient / Refinement space: REAL
Details: Homology models were generated from appropriate chain in 4HEA and 3C4S and rigid-body docked into the map using PHENIX. Remaining chains were built ab initio in COOT. All chains were iteratively refined and adjusted using PHENIX and COOT, respectively.
Input PDB model: 4HEA, 3C4S
Overall bvalue: 3
Output model

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