1CWQ

M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural alterations for proton translocation in the M state of wild-type bacteriorhodopsin.

Sass, H.J.Buldt, G.Gessenich, R.Hehn, D.Neff, D.Schlesinger, R.Berendzen, J.Ormos, P.

(2000) Nature 406: 649-653

  • DOI: 10.1038/35020607
  • Primary Citation of Related Structures:  
    1CWQ

  • PubMed Abstract: 
  • The transport of protons across membranes is an important process in cellular bioenergetics. The light-driven proton pump bacteriorhodopsin is the best-characterized protein providing this function. Photon energy is absorbed by the chromophore retinal, covalently bound to Lys 216 via a protonated Schiff base ...

    The transport of protons across membranes is an important process in cellular bioenergetics. The light-driven proton pump bacteriorhodopsin is the best-characterized protein providing this function. Photon energy is absorbed by the chromophore retinal, covalently bound to Lys 216 via a protonated Schiff base. The light-induced all-trans to 13-cis isomerization of the retinal results in deprotonation of the Schiff base followed by alterations in protonatable groups within bacteriorhodopsin. The changed force field induces changes, even in the tertiary structure, which are necessary for proton pumping. The recent report of a high-resolution X-ray crystal structure for the late M intermediate of a mutant bacteriorhopsin (with Asp 96-->Asn) displays the structure of a proton pathway highly disturbed by the mutation. To observe an unperturbed proton pathway, we determined the structure of the late M intermediate of wild-type bacteriorhodopsin (2.25 A resolution). The cytoplasmic side of our M2 structure shows a water net that allows proton transfer from the proton donor group Asp 96 towards the Schiff base. An enlarged cavity system above Asp 96 is observed, which facilitates the de- and reprotonation of this group by fluctuating water molecules in the last part of the cycle.


    Organizational Affiliation

    Institute of Structural Biology, Research Centre Jülich, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIORHODOPSIN ("M" STATE INTERMEDIATE IN COMBINATION WITH GROUND STATE)A, B248Halobacterium salinarumMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

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

Download Ideal Coordinates CCD File 
CA [auth B], FA [auth B], I [auth A], NA [auth B], S [auth A], T [auth A]TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
 Ligand Interaction
UND
Query on UND

Download Ideal Coordinates CCD File 
D [auth A], EA [auth B], GA [auth B], M [auth A], N [auth A], PA [auth B], QA [auth B], Y [auth A]UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , DA [auth B] , E [auth A] , HA [auth B] , J [auth A] , JA [auth B] , L [auth A] , 
AA [auth B],  BA [auth B],  DA [auth B],  E [auth A],  HA [auth B],  J [auth A],  JA [auth B],  L [auth A],  LA [auth B],  MA [auth B],  O [auth A],  OA [auth B],  RA [auth B],  U [auth A],  V [auth A],  X [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
HEX
Query on HEX

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , IA [auth B] , K [auth A] , KA [auth B] , P [auth A] , Q [auth A] , 
F [auth A],  G [auth A],  H [auth A],  IA [auth B],  K [auth A],  KA [auth B],  P [auth A],  Q [auth A],  R [auth A],  SA [auth B],  TA [auth B],  W [auth A]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.167 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.08α = 90
b = 61.08β = 90
c = 110.4γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance