4P3W | pdb_00004p3w

Crystal structure of the human filamin A Ig-like domains 20-21 in complex with migfilin peptide

• PDB DOI: https://doi.org/10.2210/pdb4P3W/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-03-10 Released: 2015-08-12 
• Deposition Author(s): Seppala, J., Pentikainen, U., Ylanne, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human filamin A Ig-like domains 20-21 in complex with migfilin peptide

Seppala, J., Pentikainen, U., Ylanne, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 130.81 kDa 
• Atom Count: 8,100 
• Modeled Residue Count: 1,090 
• Deposited Residue Count: 1,236 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Filamin-A	A, B, E, F, I [auth D], J [auth C]	182	Homo sapiens	Mutation(s): 0  Gene Names: FLNA, FLN, FLN1
UniProt & NIH Common Fund Data Resources
Find proteins for P21333 (Homo sapiens) Explore P21333  Go to UniProtKB:  P21333
PHAROS:  P21333 GTEx:  ENSG00000196924

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Filamin-binding LIM protein 1	C [auth G], D [auth H], G [auth K], H [auth L], K [auth J], L [auth I]	24	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUP2 (Homo sapiens) Explore Q8WUP2  Go to UniProtKB:  Q8WUP2
PHAROS:  Q8WUP2 GTEx:  ENSG00000162458

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PR	N [auth A], P [auth B], S [auth E], T [auth D]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N
SO4	M [auth A], O [auth B], Q [auth E], U [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	R [auth E], V [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.154	α = 90
b = 88.154	β = 90
c = 394.709	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Seppala, J., Pentikainen, U., Ylanne, J.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description, Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary