5G2C

The crystal structure of light-driven chloride pump ClR (T102D) mutant at pH 4.5.

• PDB DOI: https://doi.org/10.2210/pdb5G2C/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Nonlabens marinus S1-08
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-04-07 Released: 2016-10-19 
• Deposition Author(s): Kim, K.L., Kwon, S.K., Jun, S.H., Cha, J.S., Kim, H.Y., Kim, J.H., Cho, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Crystal Structure and Functional Characterization of a Light-Driven Chloride Pump Having an Ntq Motif.

Kim, K., Kwon, S., Jun, S., Cha, J.S., Kim, H., Lee, W., Kim, J.F., Cho, H.

(2016) Nat Commun 7: 12677

• PubMed: 27554809 
• DOI: https://doi.org/10.1038/ncomms12677
• Primary Citation of Related Structures:  
  5G28, 5G2A, 5G2C, 5G2D, 5G54


• PubMed Abstract: 
  

  A novel light-driven chloride-pumping rhodopsin (ClR) containing an 'NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08(T) determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a '3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B-C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications.

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Organizational Affiliation: 

Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.19 kDa 
• Atom Count: 2,245 
• Modelled Residue Count: 268 
• Deposited Residue Count: 275 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHLORIDE PUMPING RHODOPSIN	A	275	Nonlabens marinus S1-08	Mutation(s): 1  Membrane Entity: Yes
UniProt
Find proteins for W8VZW3 (Nonlabens marinus S1-08) Explore W8VZW3  Go to UniProtKB:  W8VZW3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	I [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
OLA	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], K [auth A], L [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PEG	J [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.31 Å
• R-Value Free: 0.239 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.441	α = 90
b = 50.033	β = 131.47
c = 77.786	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-19 
Deposition Author(s): Kim, K.L., Kwon, S.K., Jun, S.H., Cha, J.S., Kim, H.Y., Kim, J.H., Cho, H.S.

Revision History  

• Version 1.0: 2016-10-19
  Type: Initial release
  
• Version 1.1: 2017-03-29
  Changes: Other
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description