7VGU

Time-resolved serial femtosecond crystallography structure of light-driven chloride ion-pumping rhodopsin, NM-R3 : structure obtained 1 msec after photoexcitation with bromide ion

PDB DOI: https://doi.org/10.2210/pdb7VGU/pdb

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

Deposited: 2021-09-18 Released: 2022-02-16
Deposition Author(s): Hosaka, T., Nango, E., Nakane, T., Luo, F., Kimura-Someya, T., Shirouzu, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.211
R-Value Work: 0.182
R-Value Observed: 0.183

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.

Hosaka, T., Nomura, T., Kubo, M., Nakane, T., Fangjia, L., Sekine, S.I., Ito, T., Murayama, K., Ihara, K., Ehara, H., Kashiwagi, K., Katsura, K., Akasaka, R., Hisano, T., Tanaka, T., Tanaka, R., Arima, T., Yamashita, A., Sugahara, M., Naitow, H., Matsuura, Y., Yoshizawa, S., Tono, K., Owada, S., Nureki, O., Kimura-Someya, T., Iwata, S., Nango, E., Shirouzu, M.

(2022) Proc Natl Acad Sci U S A 119

PubMed: 35197289 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.2117433119
Primary Citation of Related Structures:
7VGT, 7VGU, 7VGV

PubMed Abstract:
Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-µs and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3.

Organizational Affiliation

RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan.

Macromolecule Content

Total Structure Weight: 32.01 kDa
Atom Count: 2,500
Modelled Residue Count: 265
Deposited Residue Count: 279
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride pumping rhodopsin	A	279	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	W8VZW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET (Subject of Investigation/LOI) Query on RET Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
D10 (Subject of Investigation/LOI) Query on D10 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]
HEX (Subject of Investigation/LOI) Query on HEX Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
BR (Subject of Investigation/LOI) Query on BR Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	J [auth A], K [auth A], L [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]