6TJV

Structure of the NDH-1MS complex from Thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Redox-coupled proton pumping drives carbon concentration in the photosynthetic complex I.

Schuller, J.M.Saura, P.Thiemann, J.Schuller, S.K.Gamiz-Hernandez, A.P.Kurisu, G.Nowaczyk, M.M.Kaila, V.R.I.

(2020) Nat Commun 11: 494-494

  • DOI: https://doi.org/10.1038/s41467-020-14347-4
  • Primary Citation of Related Structures:  
    6TJV

  • PubMed Abstract: 

    Photosynthetic organisms capture light energy to drive their energy metabolism, and employ the chemical reducing power to convert carbon dioxide (CO 2 ) into organic molecules. Photorespiration, however, significantly reduces the photosynthetic yields. To survive under low CO 2 concentrations, cyanobacteria evolved unique carbon-concentration mechanisms that enhance the efficiency of photosynthetic CO 2 fixation, for which the molecular principles have remained unknown. We show here how modular adaptations enabled the cyanobacterial photosynthetic complex I to concentrate CO 2 using a redox-driven proton-pumping machinery. Our cryo-electron microscopy structure at 3.2 Å resolution shows a catalytic carbonic anhydrase module that harbours a Zn 2+ active site, with connectivity to proton-pumping subunits that are activated by electron transfer from photosystem I. Our findings illustrate molecular principles in the photosynthetic complex I machinery that enabled cyanobacteria to survive in drastically changing CO 2 conditions.


  • Organizational Affiliation

    Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany. janschu@biochem.mpg.de.


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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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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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 4501Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKF4 (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: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL29 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 5611Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKF5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
NADH dehydrogenase subunit 6200Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DL30 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit H394Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJD9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit I196Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
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: 7.1.1
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit K237Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
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: 7.1.1
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKZ3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit M111Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
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: 7.1.1
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: 7.1.1
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
Tlr0906 protein437Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Tll0220 protein149Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DMA1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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EA [auth L],
S [auth A]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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Z [auth F]CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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DA [auth K],
FA [auth L],
U [auth D],
W [auth F],
Y [auth F]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
PGT
Query on PGT

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T [auth C],
V [auth D]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
BCR
Query on BCR

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X [auth F]BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
SF4
Query on SF4

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AA [auth I],
BA [auth I],
CA [auth K]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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GA [auth P]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)Germany715311
German Research Foundation (DFG)Germany836/3-2
German Research Foundation (DFG)Germany836/4-1
German Research Foundation (DFG)Germany836/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release