5ZTK

Synchrotron structure of light-driven chloride pump having an NTQ motif


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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 Biol Chem 294: 794-804

  • DOI: 10.1074/jbc.RA118.004038
  • Primary Citation of Related Structures:  
    5ZTL, 5ZTK

  • 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 ...

    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.


    Organizational Affiliation

    From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, wlee@spin.yonsei.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chloride pumping rhodopsinA275Nonlabens marinus S1-08Mutation(s): 0 
Gene Names: ClRNMS_1267
Find proteins for W8VZW3 (Nonlabens marinus S1-08)
Explore W8VZW3 
Go to UniProtKB:  W8VZW3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.756α = 90
b = 49.402β = 109.85
c = 69.327γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Cootmodel building
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2017R1A2B2008483
National Research Foundation (Korea)Korea, Republic OfNRF-2016R1A6A3A04010213

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references