5H2J

A three dimensional movie of structural changes in bacteriorhodopsin: structure obtained 290 ns after photoexcitation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted L2PClick on this verticalbar to view detailsBest fitted RETClick on this verticalbar to view detailsBest fitted MYSClick on this verticalbar to view detailsBest fitted C14Click on this verticalbar to view detailsBest fitted TRDClick on this verticalbar to view detailsBest fitted UNDClick on this verticalbar to view details

This is version 1.4 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: https://doi.org/10.1126/science.aah3497
  • Primary Citation of Related Structures:  
    5B6V, 5B6W, 5B6X, 5B6Y, 5B6Z, 5H2H, 5H2I, 5H2J, 5H2K, 5H2L, 5H2M, 5H2N, 5H2O, 5H2P

  • 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. 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

    RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriorhodopsin248Halobacterium salinarum NRC-1Mutation(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
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

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C [auth A],
K [auth A],
L [auth A]
2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
RET
Query on RET

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B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
MYS
Query on MYS

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I [auth A],
M [auth A]
PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
C14
Query on C14

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O [auth A]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
TRD
Query on TRD

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D [auth A]TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
UND
Query on UND

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J [auth A],
Q [auth A]
UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
D10
Query on D10

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E [auth A]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
DD9
Query on DD9

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N [auth A]nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
OCT
Query on OCT

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G [auth A],
H [auth A],
P [auth A]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HP6
Query on HP6

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F [auth A]HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 63
  • Diffraction Data: https://doi.org/10.11577/1337005
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

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted L2PClick on this verticalbar to view detailsBest fitted RETClick on this verticalbar to view detailsBest fitted MYSClick on this verticalbar to view detailsBest fitted C14Click on this verticalbar to view detailsBest fitted TRDClick on this verticalbar to view detailsBest fitted UNDClick on this verticalbar to view details

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: 2018-01-31
    Changes: Data collection
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.4: 2023-11-08
    Changes: Refinement description