5B6V

A three dimensional movie of structural changes in bacteriorhodopsin: resting state structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A three-dimensional movie of structural changes in bacteriorhodopsin

Nango, E.Royant, A.Kubo, M.Nakane, T.Wickstrand, C.Kimura, T.Tanaka, T.Tono, K.Song, C.Tanaka, R.Arima, T.Yamashita, A.Kobayashi, J.Hosaka, T.Mizohata, E.Nogly, P.Sugahara, M.Nam, D.Nomura, T.Shimamura, T.Im, D.Fujiwara, T.Yamanaka, Y.Jeon, B.Nishizawa, T.Oda, K.Fukuda, M.Andersson, R.Bath, P.Dods, R.Davidsson, J.Matsuoka, S.Kawatake, S.Murata, M.Nureki, O.Owada, S.Kameshima, T.Hatsui, T.Joti, Y.Schertler, G.Yabashi, M.Bondar, A.N.Standfuss, J.Neutze, R.Iwata, S.

(2016) Science 354: 1552-1557

  • DOI: 10.1126/science.aah3497
  • Primary Citation of Related Structures:  
    5B6Z, 5B6Y, 5B6V, 5B6X, 5B6W, 5H2P, 5H2O, 5H2H, 5H2J, 5H2I

  • PubMed Abstract: 
  • Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation ...

    Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient.


    Organizational Affiliation

    Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bacteriorhodopsin A248Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: bopVNG_1467G
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, Viral, and Unusual Rhodopsins
Protein: 
Bacteriorhodopsin (BR) 3D movie, ground state
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 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L2P
Query on L2P

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A
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
 Ligand Interaction
RET
Query on RET

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A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
MYS
Query on MYS

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A
PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
 Ligand Interaction
C14
Query on C14

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A
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
TRD
Query on TRD

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A
TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
 Ligand Interaction
UND
Query on UND

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A
UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

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A
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
DD9
Query on DD9

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A
nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

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A
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
HP6
Query on HP6

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A
HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.5α = 90
b = 62.5β = 90
c = 112γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2018-01-24
    Changes: Data collection