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- PDB-7wfy: Crystal Structure of the VAV2 SH2 domain in complex with APP phos... -

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Basic information

Entry
Database: PDB / ID: 7wfy
TitleCrystal Structure of the VAV2 SH2 domain in complex with APP phosphorylated peptide
Components
  • Amyloid beta A4 protein-binding family B member 1 (protein)
  • Guanine nucleotide exchange factor VAV2
KeywordsPROTEIN BINDING / Complex
Function / homology
Function and homology information


Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / epidermal growth factor receptor binding / regulation of cell size / RHOB GTPase cycle / small GTPase-mediated signal transduction / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK ...Azathioprine ADME / regulation of small GTPase mediated signal transduction / lamellipodium assembly / epidermal growth factor receptor binding / regulation of cell size / RHOB GTPase cycle / small GTPase-mediated signal transduction / regulation of GTPase activity / Fc-gamma receptor signaling pathway involved in phagocytosis / NRAGE signals death through JNK / RHOC GTPase cycle / Fc-epsilon receptor signaling pathway / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / EPH-ephrin mediated repulsion of cells / RAC2 GTPase cycle / RAC3 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / GPVI-mediated activation cascade / RAC1 GTPase cycle / phosphotyrosine residue binding / FCERI mediated Ca+2 mobilization / VEGFR2 mediated vascular permeability / guanyl-nucleotide exchange factor activity / Signal transduction by L1 / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / platelet activation / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / G alpha (12/13) signalling events / cellular response to xenobiotic stimulus / cell migration / DAP12 signaling / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / signal transduction / metal ion binding / plasma membrane / cytosol / cytoplasm
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. / Variant SH3 domain / Calponin homology 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. / Variant SH3 domain / Calponin homology domain / Phorbol esters/diacylglycerol binding domain (C1 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. / 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 / PH domain / 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 / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily
Similarity search - Domain/homology
Guanine nucleotide exchange factor VAV2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.449 Å
AuthorsZhang, Y.J. / Liu, Y.R. / Wu, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2022
Title: Vav2 is a novel APP-interacting protein that regulates APP protein level.
Authors: Zhang, Y. / Yang, X. / Liu, Y. / Ge, L. / Wang, J. / Sun, X. / Wu, B. / Wang, J.
History
DepositionDec 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Guanine nucleotide exchange factor VAV2
A: Amyloid beta A4 protein-binding family B member 1 (protein)


Theoretical massNumber of molelcules
Total (without water)14,8962
Polymers14,8962
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4 kcal/mol
Surface area6220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.743, 109.589, 41.369
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11C-806-

HOH

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Components

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


Mass: 13893.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52735
#2: Protein/peptide Amyloid beta A4 protein-binding family B member 1 (protein)


Mass: 1001.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 25% PEG 3350, 0.2 M Magnesium chloride hexahydrate, 0.1 M, Tris/HCl, pH 8.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.449→50 Å / Num. obs: 5538 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 36.07 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 26.33
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.347 / Num. unique obs: 272

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.10-2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MXC

3mxc


Resolution: 2.449→41.369 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2678 583 10.75 %
Rwork0.2275 4838 -
obs0.2319 5421 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.38 Å2 / Biso mean: 39.7782 Å2 / Biso min: 18.52 Å2
Refinement stepCycle: final / Resolution: 2.449→41.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms928 0 0 8 936
Biso mean---26.24 -
Num. residues----112
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008951
X-RAY DIFFRACTIONf_angle_d0.9951288
X-RAY DIFFRACTIONf_chiral_restr0.054136
X-RAY DIFFRACTIONf_plane_restr0.006163
X-RAY DIFFRACTIONf_dihedral_angle_d17.139563
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.449-2.6950.36421530.2991113295
2.695-3.08490.35361420.2994119499
3.0849-3.88620.27881430.22781228100
3.8862-41.3690.20121450.1825128498
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6403-0.0166-0.59048.4711-1.43681.89130.1820.2948-0.2135-1.2639-0.1369-0.16740.25730.2264-0.08680.29990.0647-0.02580.3835-0.07540.250714.875412.2328-6.6981
20.89632.7818-2.22381.9984-4.70816.32651.18730.9146-0.2495-1.29840.08842.1709-0.4616-1.18872.77170.94570.1655-0.20.62-0.08660.42688.78218.596-14.5665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' and resid 665 through 769)C665 - 769
2X-RAY DIFFRACTION2(chain 'A' and resid -1 through 5)A-1 - 5

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