5ZTL

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 o ...

    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

    Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720.,Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, PO Box 596, SE-751 24 Uppsala, Sweden.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158.,Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287.,Department of Chemistry, University of Cambridge, CB2 1EW Cambridge, United Kingdom.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China. Electronic address: chenzhongzhou@cau.edu.cn.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China.,Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,School of Pharmaceutical Sciences; MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing, 100084, China.,Centre de Biologie Cellulaire de Montpellier, CNRS, University Montpellier, UMR5237, 34090 Montpellier, France.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA. s-nair@life.uiuc.edu.,Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.,Department of Ophthalmology, University of California, San Francisco, CA 94158.,Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,Department of Chemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,School of Life Sciences, University of Science and Technology of China, Anhui, 230026, China.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; jfraser@fraserlab.com enogales@lbl.gov.,Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0620, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, United States.,Department of Molecular Biosciences , The University of Texas at Austin , Austin , Texas 78712 , United States.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Picobiology Institute, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea, wlee@spin.yonsei.ac.kr.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.,Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China, hgliu@csrc.ac.cn.,Department of Pharmaceutical Sciences, College of Pharmacy , University of Kentucky , 789 South Limestone Street , Lexington , Kentucky 40536 , United States.,Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, La Rioja, Spain.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA. vddonk@illinois.edu.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Champaign, IL, USA.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China.,From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea.,Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States.,Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, United States.,School of Pharmaceutical Sciences , Sun Yat-Sen University , Guangzhou 510006 , P.R. China.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chloride pumping rhodopsin
A
275Nonlabens marinus S1-08Mutation(s): 0 
Gene Names: ClR
Find proteins for W8VZW3 (Nonlabens marinus S1-08)
Go to UniProtKB:  W8VZW3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLA
Query on OLA

Download SDF File 
Download CCD File 
A
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.240 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.360α = 90.00
b = 50.090β = 109.65
c = 69.400γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHASERphasing
CrystFELdata scaling
Cootmodel building
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
National Natural Science Foundation of ChinaChina11575021, U1530401 and U1430237)

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-01-02
    Type: Data collection
  • Version 1.2: 2019-01-30
    Type: Data collection, Database references