Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 35.24 kDa 
• Atom Count: 2526 
• Modelled Residue Count: 296 
• Deposited Residue Count: 296 
• Unique protein chains: 1

3RH8

Crystal Structure of the Light-state Dimer of Fungal Blue-Light Photoreceptor Vivid

• PDB DOI: 10.2210/pdb3RH8/pdb

• Classification: CIRCADIAN CLOCK PROTEIN
• Organism(s): Neurospora crassa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-11 Released: 2011-09-21 
• Deposition Author(s): Vaidya, A.T., Crane, B.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.287 
• R-Value Work: 0.226 

Literature

Structure of a Light-Activated LOV Protein Dimer That Regulates Transcription.

Vaidya, A.T., Chen, C.H., Dunlap, J.C., Loros, J.J., Crane, B.R.

(2011) Sci Signal 4: ra50-ra50

• PubMed: 21868352 
• DOI: 10.1126/scisignal.2001945
• Primary Citation of Related Structures:  
  3RH8


• PubMed Abstract: 
  

Light, oxygen, or voltage (LOV) protein domains are present in many signaling proteins in bacteria, archaea, protists, plants, and fungi. The LOV protein VIVID (VVD) of the filamentous fungus Neurospora crassa enables the organism to adapt to constant or increasing amounts of light and facilitates proper entrainment of circadian rhythms. Here, we determined the crystal structure of the fully light-adapted VVD dimer and reveal the mechanism by which light-driven conformational change alters the oligomeric state of the protein. Light-induced formation of a cysteinyl-flavin adduct generated a new hydrogen bond network that released the amino (N) terminus from the protein core and restructured an acceptor pocket for binding of the N terminus on the opposite subunit of the dimer. Substitution of residues critical for the switch between the monomeric and the dimeric states of the protein had profound effects on light adaptation in Neurospora. The mechanism of dimerization of VVD provides molecular details that explain how members of a large family of photoreceptors convert light responses to alterations in protein-protein interactions.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vivid PAS protein VVD	A [auth B], B [auth D]	148	Neurospora crassa	Mutation(s): 0  Gene Names: vvd, G17A4.050, GE21DRAFT_9175
UniProt
Find proteins for Q9C3Y6 (Neurospora crassa) Explore Q9C3Y6  Go to UniProtKB:  Q9C3Y6

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.287 
• R-Value Work: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.647	α = 90
b = 77.473	β = 99.77
c = 54.696	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-11 
• Released Date: 2011-09-21 
Deposition Author(s): Vaidya, A.T., Crane, B.R.

Revision History  

• Version 1.0: 2011-09-21
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description