1TS8

Structure of the pR cis planar intermediate from time-resolved Laue crystallography

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.383 
  • R-Value Work: 0.353 
  • R-Value Observed: 0.356 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Visualizing reaction pathways in photoactive yellow protein from nanoseconds to seconds.

Ihee, H., Rajagopal, S., Srajer, V., Pahl, R., Anderson, S., Schmidt, M., Schotte, F., Anfinrud, P.A., Wulff, M., Moffat, K.

(2005) Proc Natl Acad Sci U S A 102: 7145-7150

  • DOI: 10.1073/pnas.0409035102
  • Primary Citation of Related Structures:  
    1TS7, 1TS6, 1TS0, 1TS8

  • PubMed Abstract: 

    • Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate ...

    Determining 3D intermediate structures during the biological action of proteins in real time under ambient conditions is essential for understanding how proteins function. Here we use time-resolved Laue crystallography to extract short-lived intermediate structures and thereby unveil signal transduction in the blue light photoreceptor photoactive yellow protein (PYP) from Halorhodospira halophila. By analyzing a comprehensive set of Laue data during the PYP photocycle (forty-seven time points from one nanosecond to one second), we track all atoms in PYP during its photocycle and directly observe how absorption of a blue light photon by its p-coumaric acid chromophore triggers a reversible photocycle. We identify a complex chemical mechanism characterized by five distinct structural intermediates. Structural changes at the chromophore in the early, red-shifted intermediates are transduced to the exterior of the protein in the late, blue-shifted intermediates through an initial "volume-conserving" isomerization of the chromophore and the progressive disruption of hydrogen bonds between the chromophore and its surrounding binding pocket. These results yield a comprehensive view of the PYP photocycle when seen in the light of previous biophysical studies on the system.

    Organizational Affiliation: 

    Department of Chemistry and School of Molecular Science (BK21), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, South Korea. hyotcherl.ihee@kaist.ac.kr



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photoactive yellow protein A125Halorhodospira halophilaMutation(s): 0 
Gene Names: pyp
Find proteins for P16113 (Halorhodospira halophila)
Explore P16113 
Go to UniProtKB:  P16113
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC4
Query on HC4
Download Ideal Coordinates CCD File 
A
4'-HYDROXYCINNAMIC ACID
C9 H8 O3
NGSWKAQJJWESNS-ZZXKWVIFSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.383 
  • R-Value Work: 0.353 
  • R-Value Observed: 0.356 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.833α = 90
b = 66.833β = 90
c = 40.947γ = 120
Software Package:
Software NamePurpose
LaueViewdata reduction
SHELXL-97refinement
LaueViewdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-09-09
    Changes: Other
  • Version 1.4: 2017-10-11
    Changes: Refinement description