7VGV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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

  • DOI: 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 ...

    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; mikako.shirouzu@riken.jp eriko.nango.c4@tohoku.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Chloride pumping rhodopsinA, B, C279Nonlabens 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download Ideal Coordinates CCD File 
D [auth A],
K [auth B],
R [auth C]
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
R16
Query on R16

Download Ideal Coordinates CCD File 
J [auth A]HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
 Ligand Interaction
C14
Query on C14

Download Ideal Coordinates CCD File 
I [auth A],
P [auth B]
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
DD9
Query on DD9

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
O [auth B]
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

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Q [auth B]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

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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
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
S [auth C],
T [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.4α = 90
b = 69.5β = 90
c = 231.4γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2022-03-09
    Changes: Database references