5B2N | pdb_00005b2n

Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus

• PDB DOI: https://doi.org/10.2210/pdb5B2N/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Nonlabens marinus S1-08
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2016-01-20 Released: 2016-07-13 
• Deposition Author(s): Hosaka, T., Kimura-Someya, T., Shirouzu, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3

Hosaka, T., Yoshizawa, S., Nakajima, Y., Ohsawa, N., Hato, M., DeLong, E.F., Kogure, K., Yokoyama, S., Kimura-Someya, T., Iwasaki, W., Shirouzu, M.

(2016) J Biological Chem 291: 17488-17495

• PubMed: 27365396 
• DOI: https://doi.org/10.1074/jbc.M116.728220
• Primary Citation Related Structures: 
  5B2N


• PubMed Abstract: 
  

  The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 Å resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities.

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Organizational Affiliation: 
• From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and.
the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan.
the Center for Microbial Oceanography, Research and Education, University of Hawaii, Honolulu, Hawaii 96822, and.
RIKEN Structural Biology Laboratory, Yokohama, Kanagawa 230-0045, Japan.
the Atmosphere and Ocean Research Institute, University of Tokyo, Chiba 277-8564, Japan, [e-mail].
the Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0032, Japan.
From the Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, and [e-mail].

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: 32.6 kDa 
• Atom Count: 2,299 
• Modeled Residue Count: 263 
• Deposited Residue Count: 279 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride pumping rhodopsin	A	279	Nonlabens marinus S1-08	Mutation(s): 0  Gene Names: ClR, NMS_1267 Membrane Entity: Yes
UniProt
Find proteins for W8VZW3 (Nonlabens marinus S1-08) Explore W8VZW3  Go to UniProtKB:  W8VZW3

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
D12	J [auth A], K [auth A], L [auth A]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10	M [auth A], N [auth A], O [auth A]	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT	F [auth A], G [auth A], H [auth A], I [auth A]	N-OCTANE C8 H18 TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX	D [auth A], E [auth A]	HEXANE C6 H14 VLKZOEOYAKHREP-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.58	α = 90
b = 49.79	β = 130.4
c = 75.32	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-13 
Deposition Author(s): Hosaka, T., Kimura-Someya, T., Shirouzu, M.

Revision History  

• Version 1.0: 2016-07-13
  Type: Initial release
  
• Version 1.1: 2016-09-07
  Changes: Database references
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary