7O8S

NmHR light state structure at 32.5 ms (30 - 35 ms) after photoexcitation determined by serial millisecond crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.294 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Dynamics and mechanism of a light-driven chloride pump.

Mous, S.Gotthard, G.Ehrenberg, D.Sen, S.Weinert, T.Johnson, P.J.M.James, D.Nass, K.Furrer, A.Kekilli, D.Ma, P.Brunle, S.Casadei, C.M.Martiel, I.Dworkowski, F.Gashi, D.Skopintsev, P.Wranik, M.Knopp, G.Panepucci, E.Panneels, V.Cirelli, C.Ozerov, D.Schertler, G.F.X.Wang, M.Milne, C.Standfuss, J.Schapiro, I.Heberle, J.Nogly, P.

(2022) Science 375: 845-851

  • DOI: https://doi.org/10.1126/science.abj6663
  • Primary Citation of Related Structures:  
    7O8F, 7O8G, 7O8H, 7O8I, 7O8J, 7O8K, 7O8L, 7O8M, 7O8N, 7O8O, 7O8P, 7O8Q, 7O8R, 7O8S, 7O8T, 7O8U, 7O8V, 7O8Y, 7O8Z

  • PubMed Abstract: 

    Chloride transport by microbial rhodopsins is an essential process for which molecular details such as the mechanisms that convert light energy to drive ion pumping and ensure the unidirectionality of the transport have remained elusive. We combined time-resolved serial crystallography with time-resolved spectroscopy and multiscale simulations to elucidate the molecular mechanism of a chloride-pumping rhodopsin and the structural dynamics throughout the transport cycle. We traced transient anion-binding sites, obtained evidence for how light energy is used in the pumping mechanism, and identified steric and electrostatic molecular gates ensuring unidirectional transport. An interaction with the π-electron system of the retinal supports transient chloride ion binding across a major bottleneck in the transport pathway. These results allow us to propose key mechanistic features enabling finely controlled chloride transport across the cell membrane in this light-powered chloride ion pump.


  • Organizational Affiliation

    Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chloride pumping rhodopsin296Nonlabens marinus S1-08Mutation(s): 0 
Gene Names: ClRNMS_1267
Membrane Entity: Yes 
UniProt
Find proteins for W8VZW3 (Nonlabens marinus S1-08)
Explore W8VZW3 
Go to UniProtKB:  W8VZW3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW8VZW3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth A]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
OLA
Query on OLA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
J [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.293 
  • R-Value Observed: 0.294 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.48α = 90
b = 51.18β = 131.78
c = 78.33γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPZ00P3_174169

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-09
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-03-09
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description