1QKR | pdb_00001qkr

Crystal structure of the vinculin tail and a pathway for activation

• PDB DOI: https://doi.org/10.2210/pdb1QKR/pdb

• Classification: ACTIN CYTOSKELETON
• Organism(s): Gallus gallus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1999-08-04 Released: 2000-08-04 
• Deposition Author(s): Bakolitsa, C., De Pereda, J.M., Bagshaw, C.R., Critchley, D.R., Liddington, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal Structure of the Vinculin Tail and a Pathway for Activation

Bakolitsa, C., De Pereda, J.M., Bagshaw, C.R., Critchley, D.R., Liddington, R.C.

(1999) Cell 99: 603

• PubMed: 10612396 
• DOI: https://doi.org/10.1016/s0092-8674(00)81549-4
• Primary Citation Related Structures: 
  1QKR


• PubMed Abstract: 
  

  Vinculin plays a dynamic role in the assembly of the actin cytoskeleton. A strong interaction between its head and tail domains that regulates binding to other cytoskeletal components is disrupted by acidic phospholipids. Here, we present the crystal structure of the vinculin tail, residues 879-1066. Five amphipathic helices form an antiparallel bundle that resembles exchangeable apolipoproteins. A C-terminal arm wraps across the base of the bundle and emerges as a hydrophobic hairpin surrounded by a collar of basic residues, adjacent to the N terminus. We show that the C-terminal arm is required for binding to acidic phospholipids but not to actin, and that binding either ligand induces conformational changes that may represent the first step in activation.

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Organizational Affiliation: 
• Department of Biochemistry, University of Leicester, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 generated by PQS (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 43.45 kDa 
• Atom Count: 3,131 
• Modeled Residue Count: 361 
• Deposited Residue Count: 376 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VINCULIN	A, B	188	Gallus gallus	Mutation(s): 9  Gene Names: VCL
UniProt
Find proteins for P12003 (Gallus gallus) Explore P12003  Go to UniProtKB:  P12003

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.248 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.6	α = 90
b = 87.77	β = 91.27
c = 50.63	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-08-04 
Deposition Author(s): Bakolitsa, C., De Pereda, J.M., Bagshaw, C.R., Critchley, D.R., Liddington, R.C.

Revision History  

• Version 1.0: 2000-08-04
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary