7RNV | pdb_00007rnv

SH2 domain of guanine nucleotide exchange factor Vav2 in complex with an actin peptide with phosphorylated tyrosine 53

PDB DOI: https://doi.org/10.2210/pdb7RNV/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-07-29 Released: 2021-08-11
Deposition Author(s): Dai, S., Horton, J.R., Cheng, X.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.272 (Depositor), 0.271 (DCC)
R-Value Work:
0.230 (Depositor), 0.229 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

The Functional Analysis of a Major Tyrosine Phosphorylation Site on Actin

Amelie, A., Dai, S., Shen, X., Horton, J.R., Zhang, X., Cheng, X.

To be published.

Macromolecule Content

Total Structure Weight: 15 kDa
Atom Count: 955
Modeled Residue Count: 110
Deposited Residue Count: 127
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide exchange factor VAV2	A	118	Homo sapiens	Mutation(s): 0 Gene Names: VAV2
UniProt & NIH Common Fund Data Resources
Find proteins for P52735 (Homo sapiens) Explore P52735 Go to UniProtKB: P52735
PHAROS: P52735 GTEx: ENSG00000160293
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P52735
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	B	9	Homo sapiens	Mutation(s): 0 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P68133 (Homo sapiens) Explore P68133 Go to UniProtKB: P68133
PHAROS: P68133 GTEx: ENSG00000143632
Entity Groups
UniProt Group	P68133
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	B	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.272 (Depositor), 0.271 (DCC)
R-Value Work: 0.230 (Depositor), 0.229 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.492	α = 90
b = 109.432	β = 90
c = 41.867	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-11

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM049245-23

Revision History (Full details and data files)

Version 1.0: 2021-08-11
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-10-16
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.