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- PDB-7rnv: SH2 domain of guanine nucleotide exchange factor Vav2 in complex ... -

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Basic information

Entry
Database: PDB / ID: 7rnv
TitleSH2 domain of guanine nucleotide exchange factor Vav2 in complex with an actin peptide with phosphorylated tyrosine 53
Components
  • Actin, alpha skeletal muscle
  • Guanine nucleotide exchange factor VAV2
KeywordsPEPTIDE BINDING PROTEIN / phosphorylated tyrosine binding protein / actin peptide
Function / homology
Function and homology information


immune response-regulating cell surface receptor signaling pathway / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / regulation of small GTPase mediated signal transduction / Azathioprine ADME / epidermal growth factor receptor binding / regulation of GTPase activity / lamellipodium assembly / RHOB GTPase cycle / small GTPase-mediated signal transduction ...immune response-regulating cell surface receptor signaling pathway / Formation of the dystrophin-glycoprotein complex (DGC) / Striated Muscle Contraction / regulation of small GTPase mediated signal transduction / Azathioprine ADME / epidermal growth factor receptor binding / regulation of GTPase activity / lamellipodium assembly / RHOB GTPase cycle / small GTPase-mediated signal transduction / NRAGE signals death through JNK / regulation of cell size / myosin binding / RHOC GTPase cycle / Fc-epsilon receptor signaling pathway / Fc-gamma receptor signaling pathway involved in phagocytosis / mesenchyme migration / CDC42 GTPase cycle / striated muscle thin filament / skeletal muscle thin filament assembly / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / GPVI-mediated activation cascade / skeletal muscle fiber development / stress fiber / phosphotyrosine residue binding / RAC1 GTPase cycle / FCERI mediated Ca+2 mobilization / muscle contraction / guanyl-nucleotide exchange factor activity / sarcomere / Signal transduction by L1 / VEGFR2 mediated vascular permeability / FCGR3A-mediated phagocytosis / actin filament / filopodium / FCERI mediated MAPK activation / ADP binding / Regulation of actin dynamics for phagocytic cup formation / platelet activation / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / VEGFA-VEGFR2 Pathway / cellular response to xenobiotic stimulus / DAP12 signaling / cell migration / G alpha (12/13) signalling events / lamellipodium / actin cytoskeleton / cell body / angiogenesis / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / hydrolase activity / positive regulation of gene expression / signal transduction / extracellular space / extracellular exosome / zinc ion binding / ATP binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
VAV2 protein, second SH3 domain / VAV2 protein, first SH3 domain / VAV2, SH2 domain / Vav, PH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / : / SOS1/NGEF-like PH domain ...VAV2 protein, second SH3 domain / VAV2 protein, first SH3 domain / VAV2, SH2 domain / Vav, PH domain / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / : / SOS1/NGEF-like PH domain / Variant SH3 domain / Calponin homology domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / ATPase, nucleotide binding domain / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Guanine nucleotide exchange factor VAV2 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsDai, S. / Horton, J.R. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245-23 United States
CitationJournal: To Be Published
Title: The Functional Analysis of a Major Tyrosine Phosphorylation Site on Actin
Authors: Amelie, A. / Dai, S. / Shen, X. / Horton, J.R. / Zhang, X. / Cheng, X.
History
DepositionJul 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide exchange factor VAV2
B: Actin, alpha skeletal muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9964
Polymers14,8722
Non-polymers1242
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-3 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.492, 109.432, 41.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Space group name HallC22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z
#8: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-915-

HOH

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Components

#1: Protein Guanine nucleotide exchange factor VAV2 / VAV-2


Mass: 13807.589 Da / Num. of mol.: 1 / Fragment: SH2 domain (UNP residues 665-774)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52735
#2: Protein/peptide Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 1063.975 Da / Num. of mol.: 1 / Fragment: UNP residues 52-60 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68133
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, pH 8.5, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.15→26.8 Å / Num. obs: 7715 / % possible obs: 96.1 % / Redundancy: 13.1 % / Biso Wilson estimate: 34.47 Å2 / CC1/2: 0.987 / Net I/σ(I): 10.3
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 5024 / CC1/2: 0.312

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IUI

2iui


Resolution: 2.15→26.8 Å / SU ML: 0.3405 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.8157
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2719 760 9.89 %
Rwork0.2297 6926 -
obs0.2339 7686 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.47 Å2
Refinement stepCycle: LAST / Resolution: 2.15→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 8 37 953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0017940
X-RAY DIFFRACTIONf_angle_d0.46481273
X-RAY DIFFRACTIONf_chiral_restr0.0432135
X-RAY DIFFRACTIONf_plane_restr0.0021161
X-RAY DIFFRACTIONf_dihedral_angle_d22.1687341
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.320.4251300.37611157X-RAY DIFFRACTION81.92
2.32-2.550.31011500.29261398X-RAY DIFFRACTION98.22
2.55-2.920.32051540.27791415X-RAY DIFFRACTION99.12
2.92-3.670.28781540.21941445X-RAY DIFFRACTION99.56
3.67-26.80.22071720.18611511X-RAY DIFFRACTION99.53

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