2VZI | pdb_00002vzi

Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex with paxillin LD4 motif

PDB DOI: https://doi.org/10.2210/pdb2VZI/pdb

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

Deposited: 2008-08-01 Released: 2008-10-28
Deposition Author(s): Lorenz, S., Vakonakis, I., Lowe, E.D., Campbell, I.D., Noble, M.E.M., Hoellerer, M.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.260 (Depositor), 0.251 (DCC)
R-Value Work:
0.205 (Depositor), 0.197 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structural analysis of the interactions between paxillin LD motifs and alpha-parvin.

Lorenz, S., Vakonakis, I., Lowe, E.D., Campbell, I.D., Noble, M.E., Hoellerer, M.K.

(2008) Structure 16: 1521-1531

PubMed: 18940607 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.str.2008.08.007
Primary Citation Related Structures:
2VZC, 2VZD, 2VZG, 2VZI

PubMed Abstract:
The adaptor protein paxillin contains five conserved leucine-rich (LD) motifs that interact with a variety of focal adhesion proteins, such as alpha-parvin. Here, we report the first crystal structure of the C-terminal calponin homology domain (CH(C)) of alpha-parvin at 1.05 A resolution and show that it is able to bind all the LD motifs, with some selectivity for LD1, LD2, and LD4. Cocrystal structures with these LD motifs reveal the molecular details of their interactions with a common binding site on alpha-parvin-CH(C), which is located at the rim of the canonical fold and includes part of the inter-CH domain linker. Surprisingly, this binding site can accommodate LD motifs in two antiparallel orientations. Taken together, these results reveal an unusual degree of binding degeneracy in the paxillin/alpha-parvin system that may facilitate the assembly of dynamic signaling complexes in the cell.

Organizational Affiliation

Laboratory of Molecular Biophysics, University of Oxford, Oxford OX1 3QU, United Kingdom.

Macromolecule Content

Total Structure Weight: 18.08 kDa
Atom Count: 1,413
Modeled Residue Count: 139
Deposited Residue Count: 151
Unique protein chains: 2

Macromolecules

Find similar proteins by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Paxillin,Paxillin	A	20	Homo sapiens	Mutation(s): 0 Gene Names: PXN
UniProt & NIH Common Fund Data Resources
Find proteins for P49023 (Homo sapiens) Explore P49023 Go to UniProtKB: P49023
PHAROS: P49023 GTEx: ENSG00000089159
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49023
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-parvin	B	131	Homo sapiens	Mutation(s): 0 Gene Names: PARVA, MXRA2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVD7 (Homo sapiens) Explore Q9NVD7 Go to UniProtKB: Q9NVD7
PHAROS: Q9NVD7 GTEx: ENSG00000197702
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NVD7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth B]	E [auth B], G [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth B] Interactions & Density Focus chain E [auth B] Focus chain G [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth B]	D [auth B], F [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain F [auth B] Interactions & Density Focus chain D [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.260 (Depositor), 0.251 (DCC)
R-Value Work: 0.205 (Depositor), 0.197 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.42	α = 90
b = 94.6	β = 90
c = 42.17	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-10-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2012-05-30
Changes: Other
Version 1.3: 2019-04-24
Changes: Data collection, Database references, Experimental preparation, Other, Source and taxonomy, Structure summary
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description