4PR9 | pdb_00004pr9

Human Vinculin (residues 891-1066) in complex with PIP

• PDB DOI: https://doi.org/10.2210/pdb4PR9/pdb

• Classification: CELL ADHESION, STRUCTURAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-03-05 Released: 2014-12-10 
• Deposition Author(s): Chinthalapudi, K., Rangarajan, E.S., Patil, D., Izard, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.250 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Mechanism and function of lipid-directed oligomerization of vinculin

Chinthalapudi, K., Rangarajan, E.S., Patil, D., Izard, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.56 kDa 
• Atom Count: 8,174 
• Modeled Residue Count: 1,033 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vinculin	A, B, C, D, E, F	176	Homo sapiens	Mutation(s): 1  Gene Names: VCL
UniProt & NIH Common Fund Data Resources
Find proteins for P18206 (Homo sapiens) Explore P18206  Go to UniProtKB:  P18206
PHAROS:  P18206 GTEx:  ENSG00000035403

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PIO	G [auth A], H [auth B], K [auth E]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C25 H49 O19 P3 XLNCEHRXXWQMPK-MJUMVPIBSA-N
GOL	I [auth B], J [auth C], L [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.250 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/560

Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.579	α = 90
b = 102.579	β = 90
c = 190.772	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Chinthalapudi, K., Rangarajan, E.S., Patil, D., Izard, T.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description