6NBY

T.elongatus NDH (composite model)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the complex I-like molecule NDH of oxygenic photosynthesis.

Laughlin, T.G.Bayne, A.N.Trempe, J.F.Savage, D.F.Davies, K.M.

(2019) Nature 566: 411-414

  • DOI: https://doi.org/10.1038/s41586-019-0921-0
  • Primary Citation of Related Structures:  
    6NBQ, 6NBX, 6NBY

  • PubMed Abstract: 

    Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis 1,2 . NAD(P)H dehydrogenase-like complex (NDH) is a key component of this pathway in most oxygenic photosynthetic organisms 3,4 and is the last large photosynthetic membrane-protein complex for which the structure remains unknown. Related to the respiratory NADH dehydrogenase complex (complex I), NDH transfers electrons originating from PSI to the plastoquinone pool while pumping protons across the thylakoid membrane, thereby increasing the amount of ATP produced per NADP + molecule reduced 4,5 . NDH possesses 11 of the 14 core complex I subunits, as well as several oxygenic-photosynthesis-specific (OPS) subunits that are conserved from cyanobacteria to plants 3,6 . However, the three core complex I subunits that are involved in accepting electrons from NAD(P)H are notably absent in NDH 3,5,6 , and it is therefore not clear how NDH acquires and transfers electrons to plastoquinone. It is proposed that the OPS subunits-specifically NdhS-enable NDH to accept electrons from its electron donor, ferredoxin 3-5,7 . Here we report a 3.1 Å structure of the 0.42-MDa NDH complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, obtained by single-particle cryo-electron microscopy. Our maps reveal the structure and arrangement of the principal OPS subunits in the NDH complex, as well as an unexpected cofactor close to the plastoquinone-binding site in the peripheral arm. The location of the OPS subunits supports a role in electron transfer and defines two potential ferredoxin-binding sites at the apex of the peripheral arm. These results suggest that NDH could possess several electron transfer routes, which would serve to maximize plastoquinone reduction and avoid deleterious off-target chemistry of the semi-plastoquinone radical.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 1372Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL32 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DL32
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 2515Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DMR6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 3132Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJ02 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DJ02
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase chain 4 1529Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKY0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 4L101Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 5656Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKX9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit J200Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit H394Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit I196Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit J168Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJ01 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit K237Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKZ4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit L76Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit M111Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DLN5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit N150Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJU2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit O70Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DMU4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-translocating NADH-quinone dehydrogenase subunit P NdhP44Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-translocating NADH-quinone dehydrogenase subunit Q NdhQ45Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Tlr0636 proteinR [auth S]110Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DL61 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0.b2
MODEL REFINEMENTPHENIX1.13

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-O5CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32GM007232-38
Department of Energy (DOE, United States)United StatesDE-SC00016240

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Database references
  • Version 1.4: 2020-04-15
    Changes: Database references