5HDS

Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 3 ps Structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein.

Pande, K.Hutchison, C.D.Groenhof, G.Aquila, A.Robinson, J.S.Tenboer, J.Basu, S.Boutet, S.DePonte, D.P.Liang, M.White, T.A.Zatsepin, N.A.Yefanov, O.Morozov, D.Oberthuer, D.Gati, C.Subramanian, G.James, D.Zhao, Y.Koralek, J.Brayshaw, J.Kupitz, C.Conrad, C.Roy-Chowdhury, S.Coe, J.D.Metz, M.Xavier, P.L.Grant, T.D.Koglin, J.E.Ketawala, G.Fromme, R.Srajer, V.Henning, R.Spence, J.C.Ourmazd, A.Schwander, P.Weierstall, U.Frank, M.Fromme, P.Barty, A.Chapman, H.N.Moffat, K.van Thor, J.J.Schmidt, M.

(2016) Science 352: 725-729

  • DOI: 10.1126/science.aad5081
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isom ...

    A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.


    Organizational Affiliation

    Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photoactive yellow protein
A
125Halorhodospira halophilaGene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Go to UniProtKB:  P16113
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
60F
Query on 60F
A
L-peptide linkingC12 H13 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.192 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 66.900α = 90.00
b = 66.900β = 90.00
c = 40.800γ = 120.00
Software Package:
Software NamePurpose
CrystFELdata reduction
REFMACrefinement
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Science Foundation (United States)United StatesNSF-0952643
National Science Foundation (United States)United StatesNSF-1231306

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2018-02-14
    Type: Data collection