5HD5 | pdb_00005hd5

Femtosecond Structural Dynamics Drives the Trans/Cis Isomerization in Photoactive Yellow Protein: 200 ns time delay photo-activated (light) structure

• PDB DOI: https://doi.org/10.2210/pdb5HD5/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Halorhodospira halophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-01-04 Released: 2016-05-25 
• Deposition Author(s): Pande, K., Tenboer, J., Schmidt, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.374 (Depositor), 0.364 (DCC) 
• R-Value Work: 
  0.289 (Depositor), 0.284 (DCC) 
• R-Value Observed: 
  0.293 (Depositor) 

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

• PubMed: 27151871 
• DOI: https://doi.org/10.1126/science.aad5081
• Primary Citation Related Structures: 
  5HD3, 5HD5, 5HDC, 5HDD, 5HDS


• 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. 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.

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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.
Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London SW7 2AZ, UK.
Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland.
Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA.
Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA.
Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany.
Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. IMPRS-UFAST, Max Planck Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA.
Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA.
Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.
Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 14.03 kDa 
• Atom Count: 1,244 
• Modeled Residue Count: 125 
• Deposited Residue Count: 125 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photoactive yellow protein	A	125	Halorhodospira halophila	Mutation(s): 0  Gene Names: pyp
UniProt
Find proteins for P16113 (Halorhodospira halophila) Explore P16113  Go to UniProtKB:  P16113

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
60F	A	L-PEPTIDE LINKING	C12 H13 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.374 (Depositor), 0.364 (DCC) 
• R-Value Work:  0.289 (Depositor), 0.284 (DCC) 
• R-Value Observed: 0.293 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1573793

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.9	α = 90
b = 66.9	β = 90
c = 40.8	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Pande, K., Tenboer, J., Schmidt, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-0952643
National Science Foundation (NSF, United States)	United States	NSF-1231306

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2018-02-14
  Changes: Data collection
• Version 1.3: 2019-11-27
  Changes: Author supporting evidence
• Version 1.4: 2023-08-16
  Changes: Data collection, Database references
• Version 1.5: 2023-11-15
  Changes: Data collection, Derived calculations