2PD8

1.8 Angstrom Crystal Structure of the Cys71Ser mutant of Vivid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational switching in the fungal light sensor Vivid

Zoltowski, B.D.Schwerdtfeger, C.Widom, J.Loros, J.J.Bilwes, A.M.Dunlap, J.C.Crane, B.R.

(2007) Science 316: 1054-1057

  • DOI: 10.1126/science.1137128
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal ...

    The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vivid PAS protein VVD
A, B
149Neurospora crassaMutation(s): 1 
Gene Names: vvd
Find proteins for Q9C3Y6 (Neurospora crassa)
Go to UniProtKB:  Q9C3Y6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.262 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.320α = 90.00
b = 80.590β = 95.60
c = 57.650γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
CNSrefinement
PDB_EXTRACTdata extraction
AMoREphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance