5ZTL | pdb_00005ztl

Non-cryogenic structure of light-driven chloride pump having an NTQ motif

• PDB DOI: https://doi.org/10.2210/pdb5ZTL/pdb

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


• Deposited: 2018-05-04 Released: 2018-12-05 
• Deposition Author(s): Yun, J.H., Park, S.Y., Liu, H., Lee, W.
• Funding Organization(s): National Research Foundation (Korea), National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.278 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.253 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

Literature

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Yun, J.H., Li, X., Park, J.H., Wang, Y., Ohki, M., Jin, Z., Lee, W., Park, S.Y., Hu, H., Li, C., Zatsepin, N., Hunter, M.S., Sierra, R.G., Koralek, J., Yoon, C.H., Cho, H.S., Weierstall, U., Tang, L., Liu, H., Lee, W.

(2019) J Biological Chem 294: 794-804

• PubMed: 30455349 
• DOI: https://doi.org/10.1074/jbc.RA118.004038
• Primary Citation Related Structures: 
  5ZTK, 5ZTL


• PubMed Abstract: 
  

  Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all- trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.

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Organizational Affiliation: 
• From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.
Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.
Department of Engineering Physics, Tsinghua University, Beijing 100086, China.
Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.
Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.
Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.
Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, [e-mail].
From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.82 kDa 
• Atom Count: 2,285 
• Modeled Residue Count: 260 
• 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	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RET	D [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N
OLA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.278 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.253 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.36	α = 90
b = 50.09	β = 109.65
c = 69.4	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Coot	model building
CrystFEL	data scaling
PHASER	phasing
PHENIX	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Yun, J.H., Park, S.Y., Liu, H., Lee, W.

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Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1A2B2008483
National Research Foundation (Korea)	Korea, Republic Of	NRF-2016R1A6A3A04010213
National Natural Science Foundation of China	China	11575021, U1530401 and U1430237)

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2019-01-02
  Changes: Data collection
• Version 1.2: 2019-01-30
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary