6A7K | pdb_00006a7k

X-ray structure of NdhS from T. elongatus

• PDB DOI: https://doi.org/10.2210/pdb6A7K/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Thermosynechococcus vestitus BP-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-03 Released: 2019-01-16 
• Deposition Author(s): Umeno, K., Misumi, Y., Tanaka, H., Kurisu, G.
• Funding Organization(s): Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.238 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structural adaptations of photosynthetic complex I enable ferredoxin-dependent electron transfer.

Schuller, J.M., Birrell, J.A., Tanaka, H., Konuma, T., Wulfhorst, H., Cox, N., Schuller, S.K., Thiemann, J., Lubitz, W., Setif, P., Ikegami, T., Engel, B.D., Kurisu, G., Nowaczyk, M.M.

(2019) Science 363: 257-260

• PubMed: 30573545 
• DOI: https://doi.org/10.1126/science.aau3613
• Primary Citation Related Structures: 
  6A7K, 6HUM


• PubMed Abstract: 
  

  Photosynthetic complex I enables cyclic electron flow around photosystem I, a regulatory mechanism for photosynthetic energy conversion. We report a 3.3-angstrom-resolution cryo-electron microscopy structure of photosynthetic complex I from the cyanobacterium Thermosynechococcus elongatus. The model reveals structural adaptations that facilitate binding and electron transfer from the photosynthetic electron carrier ferredoxin. By mimicking cyclic electron flow with isolated components in vitro, we demonstrate that ferredoxin directly mediates electron transfer between photosystem I and complex I, instead of using intermediates such as NADPH (the reduced form of nicotinamide adenine dinucleotide phosphate). A large rate constant for association of ferredoxin to complex I indicates efficient recognition, with the protein subunit NdhS being the key component in this process.

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Organizational Affiliation: 
• Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany. [e-mail] [e-mail] [e-mail].
Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany.
Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka 560-0043, Japan.
Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany.
Daiichi Sankyo Deutschland GmbH, Zielstattstr. 48, 81379 München, Germany.
Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France.
Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan. [e-mail] [e-mail] [e-mail].
Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44780 Bochum, Germany. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.57 kDa 
• Atom Count: 1,070 
• Modeled Residue Count: 121 
• Deposited Residue Count: 148 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tlr0636 protein	A, B	74	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Gene Names: tlr0636
UniProt
Find proteins for Q8DL61 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DL61  Go to UniProtKB:  Q8DL61

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	C [auth A], D [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.238 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.85	α = 90
b = 58.85	β = 90
c = 225.15	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-16 
Deposition Author(s): Umeno, K., Misumi, Y., Tanaka, H., Kurisu, G.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	--

Revision History  

• Version 1.0: 2019-01-16
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description