6KHI

Supercomplex for cylic electron transport in cyanobacteria


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for electron transport mechanism of complex I-like photosynthetic NAD(P)H dehydrogenase.

Pan, X.Cao, D.Xie, F.Xu, F.Su, X.Mi, H.Zhang, X.Li, M.

(2020) Nat Commun 11: 610-610

  • DOI: 10.1038/s41467-020-14456-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron transport from ferredoxin (Fd) to plastoquinone (PQ) and p ...

    NAD(P)H dehydrogenase-like (NDH) complex NDH-1L of cyanobacteria plays a crucial role in cyclic electron flow (CEF) around photosystem I and respiration processes. NDH-1L couples the electron transport from ferredoxin (Fd) to plastoquinone (PQ) and proton pumping from cytoplasm to the lumen that drives the ATP production. NDH-1L-dependent CEF increases the ATP/NADPH ratio, and is therefore pivotal for oxygenic phototrophs to function under stress. Here we report two structures of NDH-1L from Thermosynechococcus elongatus BP-1, in complex with one Fd and an endogenous PQ, respectively. Our structures represent the complete model of cyanobacterial NDH-1L, revealing the binding manner of NDH-1L with Fd and PQ, as well as the structural elements crucial for proper functioning of the NDH-1L complex. Together, our data provides deep insights into the electron transport from Fd to PQ, and its coupling with proton translocation in NDH-1L.


    Related Citations: 
    • Structure of photosystem from green alga.
      Su, X.,Ma, J.,Pan, X.,Zhao, X.,Chang, W.,Liu, Z.,Zhang, X.,Li, M.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing, 100049, PR China. xzzhang@ibp.ac.cn.,National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, PR China. hlmi@sibs.ac.cn.,Center for Biological Imaging, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China. xzzhang@ibp.ac.cn.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China.,National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai, 200032, PR China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China. xzzhang@ibp.ac.cn.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, PR China. meili@ibp.ac.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit 1
A
372Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhA
EC: 7.1.1.-
Find proteins for Q8DL32 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DL32
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit 2
B
515Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhB
EC: 7.1.1.-
Find proteins for Q8DMR6 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DMR6
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit 3
C
132Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhC
EC: 7.1.1.-
Find proteins for Q8DJ02 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJ02
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase chain 4 1
D
529Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhD1
EC: 7.1.1.-
Find proteins for Q8DKY0 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DKY0
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit 4L
E
101Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhE
EC: 7.1.1.-
Find proteins for Q8DL29 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DL29
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
NADH dehydrogenase subunit 5
F
656Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhF1
Find proteins for Q8DKX9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DKX9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
NADH-quinone oxidoreductase subunit J
G
200Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhG
EC: 7.1.1.-
Find proteins for Q8DL30 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DL30
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit H
H
394Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhH
EC: 7.1.1.-
Find proteins for Q8DJD9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJD9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit I
I
196Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhI
EC: 7.1.1.-
Find proteins for Q8DL31 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DL31
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit J
J
168Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhJ
EC: 7.1.1.-
Find proteins for Q8DJ01 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJ01
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit K
K
237Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhK
EC: 7.1.1.-
Find proteins for Q8DKZ4 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DKZ4
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit L
L
76Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhL
EC: 7.1.1.-
Find proteins for Q8DKZ3 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DKZ3
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit M
M
111Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhM
EC: 7.1.1.-
Find proteins for Q8DLN5 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DLN5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit N
N
150Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhN
EC: 7.1.1.-
Find proteins for Q8DJU2 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DJU2
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
NAD(P)H-quinone oxidoreductase subunit O
O
70Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: ndhO
EC: 7.1.1.-
Find proteins for Q8DMU4 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DMU4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
proton-translocating NADH-quinone dehydrogenase subunit P
P
44N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
proton-translocating NADH-quinone dehydrogenase subunit Q
Q
45N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Tlr0636 protein
S
110Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Find proteins for Q8DL61 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DL61
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Tlr0472 protein
V
146Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Find proteins for Q8DLL4 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DLL4
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Ferredoxin-1
1
98Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: petF1 (petF)
Find proteins for P0A3C9 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  P0A3C9
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
I, K
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
SQD
Query on SQD

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Download CCD File 
C, D, L
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
DGD
Query on DGD

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Download CCD File 
A
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
LMG
Query on LMG

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Download CCD File 
F
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
FES
Query on FES

Download SDF File 
Download CCD File 
1
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
BCR
Query on BCR

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Download CCD File 
D
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LHG
Query on LHG

Download SDF File 
Download CCD File 
B, C, F, I
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (China)China2017YFA0503702
Ministry of Science and Technology (China)China2017YFA0504700
Ministry of Science and Technology (China)China2016YFA0502900
Chinese Academy of SciencesChinaXDB08020302
Chinese Academy of SciencesChinaXDB08030204
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaQYZDB-SSW-SMC005
National Natural Science Foundation of ChinaChina31770778
National Natural Science Foundation of ChinaChina31600609

Revision History 

  • Version 1.0: 2020-02-12
    Type: Initial release