[English] 日本語
Yorodumi
- EMDB-0281: Structure of the photosynthetic complex I from Thermosynechococcu... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 0281
TitleStructure of the photosynthetic complex I from Thermosynechococcus elongatus
Map dataStructure of the photosynthetic complex I from Cyanobacteria
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 / homologyNADH-quinone oxidoreductase chain 4 / Cyanobacterial and plastid NDH-1 subunit M / 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 chain 4 / Cyanobacterial and plastid NDH-1 subunit M / 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 / NAD(P)H-quinone oxidoreductase subunit D/H / NAD(P)H-quinone oxidoreductase subunit 3, bacterial/plastid / NADH-quinone oxidoreductase, chain I / [NiFe]-hydrogenase, large subunit / NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily / 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-quinone oxidoreductase, chain M/4 / NADH dehydrogenase, subunit C / NADH ubiquinone oxidoreductase, 20 Kd subunit / NAD(P)H-quinone oxidoreductase, subunit N/subunit 2 / 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 dehydrogenase transmembrane 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 / NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus / Translocases, Catalysing the translocation of hydrons, Linked to oxidoreductase reactions / Oxidoreductases, Acting on NADH or NADPH, With a quinone or similar compound as acceptor / NADH dehydrogenase (quinone) / 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 / NAD(P)H-quinone oxidoreductase subunit 2 / NAD(P)H-quinone oxidoreductase subunit 4L / 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 3 / 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 J / NAD(P)H-quinone oxidoreductase subunit O
Function and homology information
SourceThermosynechococcus elongatus (strain BP-1) (Cyanobacteria) / Thermosynechococcus elongatus BP-1 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / 3.34 Å resolution
AuthorsSchuller JM / Schuller SK / Kurisu G / Engel BD / Nowaczyk MM
CitationJournal: Science / Year: 2018
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 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-Å resolution cryo-EM structure of ...Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-Å resolution cryo-EM 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. 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
DateDeposition: Oct 9, 2018 / Header (metadata) release: Jan 9, 2019 / Map release: Jan 9, 2019 / Last update: Jan 9, 2019

-
Structure visualization

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

Downloads & links

-
Map

Fileemd_0281.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.35 Å/pix.
= 405. Å
300 pix
1.35 Å/pix.
= 405. Å
300 pix
1.35 Å/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 Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.22975716 - 0.65928394
Average (Standard dev.)0.00009466233 (0.0068258634)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 405.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.2300.6590.000

-
Supplemental data

-
Sample components

+
Entire photosynthetic complex I

EntireName: photosynthetic complex I / Number of components: 22

+
Component #1: protein, photosynthetic complex I

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

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
Component #20: ligand, BETA-CAROTENE

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

+
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

+
Component #22: ligand, IRON/SULFUR CLUSTER

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

-
Experimental details

-
Sample preparation

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

-
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)

-
Image processing

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

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more