Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.06 kDa 
• Atom Count: 2094 
• Modelled Residue Count: 263 
• Deposited Residue Count: 310 
• Unique protein chains: 3

2XQN

Complex of the 2nd and 3rd LIM domains of TES with the EVH1 DOMAIN of MENA and the N-Terminal domain of actin-like protein Arp7A

• DOI: 10.2210/pdb2XQN/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-03 Released: 2011-01-26 
• Deposition Author(s): Knowles, P.P., Briggs, D.C., Murray-Rust, J., McDonald, N.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Literature

Molecular recognition of the Tes LIM2-3 domains by the actin-related protein Arp7A.

Boeda, B., Knowles, P.P., Briggs, D.C., Murray-Rust, J., Soriano, E., Garvalov, B.K., McDonald, N.Q., Way, M.

(2011) J Biol Chem 286: 11543-11554

• PubMed: 21278383 
• DOI: 10.1074/jbc.M110.171264
• Primary Citation of Related Structures:  
  2XQN


• PubMed Abstract: 
  

Actin-related proteins (Arps) are a highly conserved family of proteins that have extensive sequence and structural similarity to actin. All characterized Arps are components of large multimeric complexes associated with chromatin or the cytoskeleton. In addition, the human genome encodes five conserved but largely uncharacterized "orphan" Arps, which appear to be mostly testis-specific. Here we show that Arp7A, which has 43% sequence identity with β-actin, forms a complex with the cytoskeletal proteins Tes and Mena in the subacrosomal layer of round spermatids. The N-terminal 65-residue extension to the actin-like fold of Arp7A interacts directly with Tes. The crystal structure of the 1-65(Arp7A)·LIM2-3(Tes)·EVH1(Mena) complex reveals that residues 28-49 of Arp7A contact the LIM2-3 domains of Tes. Two alanine residues from Arp7A that occupy equivalent apolar pockets in both LIM domains as well as an intervening GPAK linker that binds the LIM2-3 junction are critical for the Arp7A-Tes interaction. Equivalent occupied apolar pockets are also seen in the tandem LIM domain structures of LMO4 and Lhx3 bound to unrelated ligands. Our results indicate that apolar pocket interactions are a common feature of tandem LIM domain interactions, but ligand specificity is principally determined by the linker sequence.

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Organizational Affiliation: 

Cell Motility Laboratory, Cancer Research UK, London Research Institute, London, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIN-LIKE PROTEIN 7A	A	65	Homo sapiens	Mutation(s): 0  Gene Names: ACTL7A
Find proteins for Q9Y615 (Homo sapiens) Explore Q9Y615  Go to UniProtKB:  Q9Y615
NIH Common Fund Data Resources
PHAROS:  Q9Y615 GTEx:  ENSG00000187003

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ENABLED HOMOLOG	B [auth M]	119	Homo sapiens	Mutation(s): 0  Gene Names: ENAH, MENA
Find proteins for Q8N8S7 (Homo sapiens) Explore Q8N8S7  Go to UniProtKB:  Q8N8S7
NIH Common Fund Data Resources
PHAROS:  Q8N8S7 GTEx:  ENSG00000154380

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TESTIN	C [auth T]	126	Homo sapiens	Mutation(s): 0  Gene Names: TES
Find proteins for Q9UGI8 (Homo sapiens) Explore Q9UGI8  Go to UniProtKB:  Q9UGI8
NIH Common Fund Data Resources
PHAROS:  Q9UGI8 GTEx:  ENSG00000135269

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth T], E [auth T], F [auth T], G [auth T], H [auth T]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.829	α = 90
b = 86.791	β = 90
c = 115.266	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-09-03 
• Released Date: 2011-01-26 
Deposition Author(s): Knowles, P.P., Briggs, D.C., Murray-Rust, J., McDonald, N.Q.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-08-24
  Changes: Database references, Other, Structure summary, Version format compliance
• Version 1.2: 2017-06-28
  Changes: Data collection
• Version 1.3: 2018-02-28
  Changes: Database references, Structure summary
• Version 1.4: 2019-05-08
  Changes: Data collection, Experimental preparation