7ZND | pdb_00007znd

Crystal structure of the light-driven inward proton pump xenorhodopsin BcXeR in the M state at pH 7.6 in the absence of sodium at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.282 (Depositor) 
  • R-Value Work: 
    0.249 (Depositor) 
  • R-Value Observed: 
    0.251 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZND

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Mechanisms of inward transmembrane proton translocation.

Kovalev, K.Tsybrov, F.Alekseev, A.Shevchenko, V.Soloviov, D.Siletsky, S.Bourenkov, G.Agthe, M.Nikolova, M.von Stetten, D.Astashkin, R.Bukhdruker, S.Chizhov, I.Royant, A.Kuzmin, A.Gushchin, I.Rosselli, R.Rodriguez-Valera, F.Ilyinskiy, N.Rogachev, A.Borshchevskiy, V.Schneider, T.R.Bamberg, E.Gordeliy, V.

(2023) Nat Struct Mol Biol 30: 970-979

  • DOI: https://doi.org/10.1038/s41594-023-01020-9
  • Primary Citation Related Structures: 
    7ZMY, 7ZN0, 7ZN3, 7ZN8, 7ZN9, 7ZNA, 7ZNB, 7ZNC, 7ZND, 7ZNE, 7ZNG, 7ZNH, 7ZNI

  • PubMed Abstract: 

    Proton transport is indispensable for cell life. It is believed that molecular mechanisms of proton movement through different types of proton-conducting molecules have general universal features. However, elucidation of such mechanisms is a challenge. It requires true-atomic-resolution structures of all key proton-conducting states. Here we present a comprehensive function-structure study of a light-driven bacterial inward proton pump, xenorhodopsin, from Bacillus coahuilensis in all major proton-conducting states. The structures reveal that proton translocation is based on proton wires regulated by internal gates. The wires serve as both selectivity filters and translocation pathways for protons. The cumulative results suggest a general concept of proton translocation. We demonstrate the use of serial time-resolved crystallography at a synchrotron source with sub-millisecond resolution for rhodopsin studies, opening the door for principally new applications. The results might also be of interest for optogenetics since xenorhodopsins are the only alternative tools to fire neurons.


  • Organizational Affiliation
    • European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 96.58 kDa 
  • Atom Count: 6,178 
  • Modeled Residue Count: 668 
  • Deposited Residue Count: 687 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
xenorhodopsin
A, B, C
229Bacillus coahuilensisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0AA82WPB4 (Bacillus coahuilensis)
Explore A0AA82WPB4 
Go to UniProtKB:  A0AA82WPB4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA82WPB4
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
GB [auth C]
J [auth A]
JA [auth B]
KB [auth C]
LA [auth B]
GB [auth C],
J [auth A],
JA [auth B],
KB [auth C],
LA [auth B],
MA [auth B],
N [auth A],
U [auth A],
XA [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
LFA

Query on LFA



Download:Ideal Coordinates CCD File
BA [auth B]
BB [auth C]
CB [auth C]
D [auth A]
DB [auth C]
BA [auth B],
BB [auth C],
CB [auth C],
D [auth A],
DB [auth C],
E [auth A],
EA [auth B],
EB [auth C],
FA [auth B],
FB [auth C],
G [auth A],
H [auth A],
HB [auth C],
JB [auth C],
M [auth A],
MB [auth C],
NA [auth B],
NB [auth C],
OA [auth B],
OB [auth C],
PA [auth B],
PB [auth C],
Q [auth A],
QA [auth B],
QB [auth C],
R [auth A],
RA [auth B],
RB [auth C],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
UA [auth B],
V [auth B],
VA [auth B],
W [auth B],
WA [auth B],
X [auth B],
Y [auth B],
YA [auth C],
Z [auth B],
ZA [auth C]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
OLA

Query on OLA



Download:Ideal Coordinates CCD File
AA [auth B]
AB [auth C]
CA [auth B]
DA [auth B]
F [auth A]
AA [auth B],
AB [auth C],
CA [auth B],
DA [auth B],
F [auth A],
GA [auth B],
HA [auth B],
I [auth A],
IA [auth B],
IB [auth C],
K [auth A],
KA [auth B],
L [auth A],
O [auth A],
P [auth A]
OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
LB [auth C]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, B, C
L-PEPTIDE LINKINGC6 H11 N O3 SMET
LYR
Query on LYR
A, B, C
L-PEPTIDE LINKINGC26 H42 N2 O2LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.282 (Depositor) 
  • R-Value Work:  0.249 (Depositor) 
  • R-Value Observed: 0.251 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.095α = 90
b = 109.364β = 90
c = 119.311γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agence Nationale de la Recherche (ANR)FranceANR-15-CE11-0029-02

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-07-12
    Changes: Database references
  • Version 1.2: 2023-07-26
    Changes: Database references, Refinement description
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description