6GA4 | pdb_00006ga4

Bacteriorhodopsin, 1 ps state, real-space refined against 15% extrapolated map


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.218 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6GA4

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.

Nass Kovacs, G.Colletier, J.P.Grunbein, M.L.Yang, Y.Stensitzki, T.Batyuk, A.Carbajo, S.Doak, R.B.Ehrenberg, D.Foucar, L.Gasper, R.Gorel, A.Hilpert, M.Kloos, M.Koglin, J.E.Reinstein, J.Roome, C.M.Schlesinger, R.Seaberg, M.Shoeman, R.L.Stricker, M.Boutet, S.Haacke, S.Heberle, J.Heyne, K.Domratcheva, T.Barends, T.R.M.Schlichting, I.

(2019) Nat Commun 10: 3177-3177

  • DOI: https://doi.org/10.1038/s41467-019-10758-0
  • Primary Citation Related Structures: 
    6GA1, 6GA2, 6GA3, 6GA4, 6GA5, 6GA6, 6GA7, 6GA8, 6GA9, 6GAA, 6GAB, 6GAC, 6GAD, 6GAE, 6GAF, 6GAG, 6GAH, 6GAI, 6RMK

  • PubMed Abstract: 

    Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins.


  • Organizational Affiliation
    • Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.

Macromolecule Content 

  • Total Structure Weight: 30.79 kDa 
  • Atom Count: 3,907 
  • Modeled Residue Count: 231 
  • Deposited Residue Count: 249 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacteriorhodopsin249Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: bopVNG_1467G
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
L2P

Query on L2P



Download:Ideal Coordinates CCD File
C [auth A],
K [auth A],
L [auth A]
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
RET

Query on RET



Download:Ideal Coordinates CCD File
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
MYS

Query on MYS



Download:Ideal Coordinates CCD File
I [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
C14

Query on C14



Download:Ideal Coordinates CCD File
N [auth A]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
TRD

Query on TRD



Download:Ideal Coordinates CCD File
D [auth A]TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
UND

Query on UND



Download:Ideal Coordinates CCD File
J [auth A],
P [auth A]
UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
D10

Query on D10



Download:Ideal Coordinates CCD File
E [auth A]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
DD9

Query on DD9



Download:Ideal Coordinates CCD File
M [auth A]nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
OCT

Query on OCT



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
O [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HP6

Query on HP6



Download:Ideal Coordinates CCD File
F [auth A]HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.218 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.201 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.7α = 90
b = 61.7β = 90
c = 109.3γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Structure summary