1DVP

CRYSTAL STRUCTURE OF THE VHS AND FYVE TANDEM DOMAINS OF HRS, A PROTEIN INVOLVED IN MEMBRANE TRAFFICKING AND SIGNAL TRANSDUCTION

• PDB DOI:  https://doi.org/10.2210/pdb1DVP/pdb

• Classification: TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-21 Released: 2000-03-06 
• Deposition Author(s): Mao, Y., Nickitenko, A., Duan, X., Lloyd, T.E., Wu, M.N., Bellen, H., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.254 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 

Literature

Crystal structure of the VHS and FYVE tandem domains of Hrs, a protein involved in membrane trafficking and signal transduction.

Mao, Y., Nickitenko, A., Duan, X., Lloyd, T.E., Wu, M.N., Bellen, H., Quiocho, F.A.

(2000) Cell 100: 447-456

• PubMed: 10693761 
• DOI: https://doi.org/10.1016/s0092-8674(00)80680-7
• Primary Citation of Related Structures:  
  1DVP


• PubMed Abstract: 
  

We have determined the 2 A X-ray structure of the 219-residue N-terminal VHS and FYVE tandem domain unit of Drosophila Hrs. The unit assumes a pyramidal structure in which the much larger VHS domain (residues 1-153) forms a rectangular base and the FYVE domain occupies the apical end. The VHS domain is comprised of an unusual "superhelix" of eight alpha helices, and the FYVE domain is mainly built of loops, two double-stranded antiparallel sheets, and a helix stabilized by two tetrahedrally coordinated zinc atoms. The two-domain structure forms an exact 2-fold-related homodimer through antiparallel association of mainly FYVE domains. Dimerization creates two identical pockets designed for binding ligands with multiple negative charges such as citrate or phosphatidylinositol 3-phosphate.

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Organizational Affiliation: 

Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas 77030, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.44 kDa 
• Atom Count: 1,980 
• Modelled Residue Count: 217 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE GROWTH FACTOR-REGULATED TYROSINE KINASE SUBSTRATE	A	220	Drosophila melanogaster	Mutation(s): 0  Gene Names: Hrs, CG2903
UniProt
Find proteins for Q960X8 (Drosophila melanogaster) Explore Q960X8  Go to UniProtKB:  Q960X8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.254 
• R-Value Work: 0.215 
• R-Value Observed: 0.219 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.706	α = 90
b = 69.665	β = 94.77
c = 41.799	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-06 
Deposition Author(s): Mao, Y., Nickitenko, A., Duan, X., Lloyd, T.E., Wu, M.N., Bellen, H., Quiocho, F.A.

Revision History  

• Version 1.0: 2000-03-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance