7VGV | pdb_00007vgv

Anion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure determined by serial femtosecond crystallography at SACLA

PDB DOI: https://doi.org/10.2210/pdb7VGV/pdb

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

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: 2.30 Å
R-Value Free:
0.241 (Depositor), 0.221 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.211 (Depositor)

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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.2117433119
Primary Citation 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: 94.7 kDa
Atom Count: 6,440
Modeled Residue Count: 791
Deposited Residue Count: 837
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chloride pumping rhodopsin	A, B, C	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	W8VZW3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] SDF format, chain R [auth C] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth C] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth C]	D [auth A], K [auth B], R [auth C]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B] Focus chain R [auth C] Interactions & Density Focus chain D [auth A] Focus chain K [auth B] Focus chain R [auth C]
R16 Query on R16 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A] mmCIF format, chain J [auth A]	J [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
C14 Query on C14 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain P [auth B]	I [auth A], P [auth B]	TETRADECANE C₁₄ H₃₀ BGHCVCJVXZWKCC-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain P [auth B] Interactions & Density Focus chain I [auth A] Focus chain P [auth B]
DD9 Query on DD9 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	G [auth A], H [auth A], O [auth B]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B]
OCT Query on OCT Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain Q [auth B]	Q [auth B]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Interactions & Density Focus chain Q [auth B]
HEX Query on HEX Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain U [auth C] SDF format, chain N [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] MOL2 format, chain N [auth B] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C] mmCIF format, chain N [auth B] mmCIF format, chain L [auth B]	E [auth A] F [auth A] L [auth B] M [auth B] N [auth B] E [auth A], F [auth A], L [auth B], M [auth B], N [auth B], U [auth C]	HEXANE C₆ H₁₄ VLKZOEOYAKHREP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C]	S [auth C], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth C] Focus chain T [auth C] Interactions & Density Focus chain S [auth C] Focus chain T [auth C]