Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.56 kDa 
• Atom Count: 2944 
• Residue Count: 298 
• Unique protein chains: 1

3D72

1.65 Angstrom crystal structure of the Cys71Val variant in the fungal photoreceptor VVD

• DOI: 10.2210/pdb3D72/pdb

• Classification: SIGNALING PROTEIN
• Mutation(s): Yes 


• Deposited: 2008-05-20 Released: 2008-06-17 
• Deposition Author(s): Zoltowski, B.D., Crane, B.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.260 
• R-Value Work: 0.250 
• R-Value Observed: 0.260 

Literature

Light activation of the LOV protein vivid generates a rapidly exchanging dimer.

Zoltowski, B.D., Crane, B.R.

(2008) Biochemistry 47: 7012-7019

• PubMed: 18553928 
• DOI: 10.1021/bi8007017
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The fungal photoreceptor Vivid (VVD) plays an important role in the adaptation of blue-light responses in Neurospora crassa. VVD, an FAD-binding LOV (light, oxygen, voltage) protein, couples light-induced cysteinyl adduct formation at the flavin ring to conformational changes in the N-terminal cap (Ncap) of the VVD PAS domain. Size-exclusion chromatography (SEC), equilibrium ultracentrifugation, and static and dynamic light scattering show that these conformational changes generate a rapidly exchanging VVD dimer, with an expanded hydrodynamic radius. A three-residue N-terminal beta-turn that assumes two different conformations in a crystal structure of a VVD C71V variant is essential for light-state dimerization. Residue substitutions at a critical hinge between the Ncap and PAS core can inhibit or enhance dimerization, whereas a Tyr to Trp substitution at the Ncap-PAS interface stabilizes the light-state dimer. Cross-linking through engineered disulfides indicates that the light-state dimer differs considerably from the dark-state dimer found in VVD crystal structures. These results verify the role of Ncap conformational changes in gating the photic response of N. crassa and indicate that LOV-LOV homo- or heterodimerization may be a mechanism for regulating light-activated gene expression.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Vivid PAS protein VVD	A, B	149	N/A	Mutation(s): 1  Gene Names: vvd, G17A4.050
Find proteins for Q9C3Y6 (Neurospora crassa) Go to UniProtKB:  Q9C3Y6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.260 
• R-Value Work: 0.250 
• R-Value Observed: 0.260 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.24	α = 90
b = 80.7	β = 95.16
c = 57.58	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-20 
• Released Date: 2008-06-17 
Deposition Author(s): Zoltowski, B.D., Crane, B.R.

Revision History 

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-06-27
  Changes: Data collection, Database references