6NBQ

T.elongatus NDH (data-set 1)


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 1.3 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: 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 ...

    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

    Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. KMDavies@lbl.gov.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit HA [auth H]394Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhHtlr1288
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJD9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DJD9
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit JB [auth J]168Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhJtlr1430
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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit KC [auth K]237Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhKtlr0705
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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit ID [auth I]196Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhItlr0668
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL31 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit NE [auth N]150Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhNtlr1130
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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UniProt GroupQ8DJU2
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit LF [auth L]76Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhLtsr0706
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit MG [auth M]111Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhMtll0447
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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit OH [auth O]70Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhOtsl0017
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: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Tlr0636 proteinI [auth S]110Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: tlr0636
UniProt
Find proteins for Q8DL61 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
NdhAJ [auth A]372Thermosynechococcus vestitus BP-1Mutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 3K [auth C]132Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhCtlr1429
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: 12
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 4LL [auth E]101Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhE
EC: 1.6.5 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proton-translocating NADH-quinone dehydrogenase subunit P NdhPM [auth P]44Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for V5V507 (Thermosynechococcus sp. NK55a)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 5N [auth F]656Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhF1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKX9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase chain 4 1O [auth D]529Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhD1tll0719
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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UniProt GroupQ8DKY0
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit 2P [auth B]515Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhBtll0045
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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UniProt GroupQ8DMR6
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
NADH-quinone oxidoreductase subunit JQ [auth G]200Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ndhG
EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL30 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
R [auth K],
S [auth I],
T [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

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: 2019-12-18
    Changes: Other