7O8P | pdb_00007o8p

NmHR light state structure at 17.5 ms (15 - 20 ms) after photoexcitation determined by serial millisecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb7O8P/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Nonlabens marinus S1-08
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2021-04-15 Released: 2022-02-09 
• Deposition Author(s): Mous, S., Gotthard, G., Ehrenberg, D., Sen, S., James, D., Johnson, P., Weinert, T., Nass, K., Furrer, A., Kekilli, D., Ma, P., Bruenle, S., Casadei, C., Martiel, I., Dworkowski, F., Gashi, D., Skopintsev, P., Wranik, M., Knopp, G., Panepucci, E., Panneels, V., Cirelli, C., Ozerov, D., Schertler, G., Wang, M., Milne, C., Standfuss, J., Schapiro, I., Heberle, J., Nogly, P.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.295 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.254 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

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

• PubMed: 35113649 
• DOI: https://doi.org/10.1126/science.abj6663
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Zürich, Switzerland.
Laboratory of Biomolecular Research, Biology and Chemistry Division, Paul Scherrer Institute, Villigen PSI, Switzerland.
Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany.
Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
Laboratory of Nonlinear Optics, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland.
Laboratory of Femtochemistry, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland.
Laboratory for Macromolecules and Bioimaging, Photon Science Division, Paul Scherrer Institute, Villigen PSI, Switzerland.
Science IT, Paul Scherrer Institute, Villigen PSI, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.32 kDa 
• Atom Count: 2,276 
• Modeled Residue Count: 263 
• Deposited Residue Count: 296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride pumping rhodopsin	A	296	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	C [auth A], D [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
RET	B [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]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.295 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.254 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.48	α = 90
b = 51.18	β = 131.78
c = 78.33	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Mous, S., Gotthard, G., Ehrenberg, D., Sen, S., James, D., Johnson, P., Weinert, T., Nass, K., Furrer, A., Kekilli, D., Ma, P., Bruenle, S., Casadei, C., Martiel, I., Dworkowski, F., Gashi, D., Skopintsev, P., Wranik, M., Knopp, G., Panepucci, E., Panneels, V., Cirelli, C., Ozerov, D., Schertler, G., Wang, M., Milne, C., Standfuss, J., Schapiro, I., Heberle, J., Nogly, P.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	PZ00P3_174169

Revision History  

• 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
• Version 1.4: 2024-10-23
  Changes: Structure summary