6L7P

cryo-EM structure of cyanobacteria NDH-1LdelV complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural insights into NDH-1 mediated cyclic electron transfer.

Zhang, C.Shuai, J.Ran, Z.Zhao, J.Wu, Z.Liao, R.Wu, J.Ma, W.Lei, M.

(2020) Nat Commun 11: 888-888

  • DOI: https://doi.org/10.1038/s41467-020-14732-z
  • Primary Citation of Related Structures:  
    6L7O, 6L7P

  • PubMed Abstract: 

    NDH-1 is a key component of the cyclic-electron-transfer around photosystem I (PSI CET) pathway, an important antioxidant mechanism for efficient photosynthesis. Here, we report a 3.2-Å-resolution cryo-EM structure of the ferredoxin (Fd)-NDH-1L complex from the cyanobacterium Thermosynechococcus elongatus. The structure reveals three β-carotene and fifteen lipid molecules in the membrane arm of NDH-1L. Regulatory oxygenic photosynthesis-specific (OPS) subunits NdhV, NdhS and NdhO are close to the Fd-binding site whilst NdhL is adjacent to the plastoquinone (PQ) cavity, and they play different roles in PSI CET under high-light stress. NdhV assists in the binding of Fd to NDH-1L and accelerates PSI CET in response to short-term high-light exposure. In contrast, prolonged high-light irradiation switches on the expression and assembly of the NDH-1MS complex, which likely contains no NdhO to further accelerate PSI CET and reduce ROS production. We propose that this hierarchical mechanism is necessary for the survival of cyanobacteria in an aerobic environment.


  • Organizational Affiliation

    Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200125, Shanghai, China.


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
NAD(P)H-quinone oxidoreductase chain 4 1529Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 7.1.1
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: 7.1.1
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: 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
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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
Find proteins for Q8DL31 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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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
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: 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
NAD(P)H-quinone oxidoreductase subunit P44Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for V5V507 (Thermosynechococcus sp. NK55a)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
NAD(P)H-quinone oxidoreductase subunit Q45Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for V5V791 (Thermosynechococcus sp. NK55a)
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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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UniProt GroupQ8DL61
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AJP
Query on AJP

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
CB [auth D]
DA [auth B]
DB [auth D]
AB [auth D],
BB [auth D],
CB [auth D],
DA [auth B],
DB [auth D],
DC [auth Q],
EA [auth B],
EB [auth D],
EC [auth Q],
FA [auth B],
FB [auth D],
FC [auth Q],
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
JB [auth F],
KA [auth B],
KB [auth F],
LA [auth B],
LB [auth F],
MA [auth B],
MB [auth F],
NA [auth B],
NB [auth F],
OA [auth C],
OB [auth F],
PA [auth C],
PB [auth F],
QB [auth F],
RB [auth F],
TB [auth G],
UB [auth G],
VB [auth G],
WA [auth D],
WB [auth G],
X [auth A],
XA [auth D],
XB [auth G],
Y [auth A],
YA [auth D],
YB [auth G],
Z [auth A],
ZA [auth D]
Digitonin
C56 H92 O29
UVYVLBIGDKGWPX-KUAJCENISA-N
DGD
Query on DGD

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V [auth A],
W [auth A]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
SQD
Query on SQD

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CC [auth L],
IB [auth F],
UA [auth D],
VA [auth D]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LHG
Query on LHG

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BA [auth B]
CA [auth B]
GB [auth F]
HB [auth F]
SA [auth D]
BA [auth B],
CA [auth B],
GB [auth F],
HB [auth F],
SA [auth D],
SB [auth G],
T [auth A],
TA [auth D],
U [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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QA [auth D],
RA [auth D],
S [auth A]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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AA [auth B]PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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AC [auth I],
BC [auth K],
ZB [auth I]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 2.0: 2021-09-22
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-05-29
    Changes: Data collection