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- PDB-4roj: Crystal Structure of the VAV2 SH2 domain in complex with TXNIP ph... -

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Basic information

Entry
Database: PDB / ID: 4roj
TitleCrystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide
Components
  • Guanine nucleotide exchange factor VAV2
  • Thioredoxin-interacting protein
KeywordsLIGASE / structural genomics / SH2 domain / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cell division / enzyme inhibitor activity / Azathioprine ADME / regulation of small GTPase mediated signal transduction / Regulation of FOXO transcriptional activity by acetylation / lamellipodium assembly / regulation of cell size / small GTPase-mediated signal transduction ...cellular response to tumor cell / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cell division / enzyme inhibitor activity / Azathioprine ADME / regulation of small GTPase mediated signal transduction / Regulation of FOXO transcriptional activity by acetylation / lamellipodium assembly / regulation of cell size / small GTPase-mediated signal transduction / RHOB GTPase cycle / epidermal growth factor receptor binding / regulation of GTPase activity / NRAGE signals death through JNK / Fc-gamma receptor signaling pathway involved in phagocytosis / RHOC GTPase cycle / Fc-epsilon receptor signaling pathway / CDC42 GTPase cycle / The NLRP3 inflammasome / platelet-derived growth factor receptor signaling pathway / RHOG GTPase cycle / EPH-ephrin mediated repulsion of cells / RHOA GTPase cycle / RAC3 GTPase cycle / RAC2 GTPase cycle / response to glucose / vascular endothelial growth factor receptor signaling pathway / Purinergic signaling in leishmaniasis infection / response to mechanical stimulus / keratinocyte differentiation / GPVI-mediated activation cascade / RAC1 GTPase cycle / phosphotyrosine residue binding / FCERI mediated Ca+2 mobilization / guanyl-nucleotide exchange factor activity / VEGFR2 mediated vascular permeability / response to progesterone / Signal transduction by L1 / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / response to hydrogen peroxide / Cytoprotection by HMOX1 / Regulation of actin dynamics for phagocytic cup formation / platelet activation / VEGFA-VEGFR2 Pathway / response to calcium ion / protein import into nucleus / G alpha (12/13) signalling events / cell migration / cellular response to xenobiotic stimulus / protein transport / response to estradiol / DAP12 signaling / regulation of cell population proliferation / angiogenesis / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to xenobiotic stimulus / cell cycle / inflammatory response / positive regulation of apoptotic process / ubiquitin protein ligase binding / negative regulation of transcription by RNA polymerase II / 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 / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal 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 / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Arrestin-like, C-terminal / Variant SH3 domain / Calponin homology domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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. / SH2 domain / SHC Adaptor Protein / 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 / Immunoglobulin E-set / PH-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Guanine nucleotide exchange factor VAV2 / Thioredoxin-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLiu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the VAV2 SH2 domain in complex with TXNIP phosphorylated peptide
Authors: Liu, Y. / Tempel, W. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Min, J. / Structural Genomics Consortium (SGC)
History
DepositionOct 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Guanine nucleotide exchange factor VAV2
B: Guanine nucleotide exchange factor VAV2
C: Guanine nucleotide exchange factor VAV2
D: Thioredoxin-interacting protein
E: Thioredoxin-interacting protein
F: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)45,59420
Polymers45,5946
Non-polymers014
Water2,612145
1
A: Guanine nucleotide exchange factor VAV2
D: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)15,1986
Polymers15,1982
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-9 kcal/mol
Surface area6300 Å2
MethodPISA
2
B: Guanine nucleotide exchange factor VAV2
E: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)15,1987
Polymers15,1982
Non-polymers05
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-9 kcal/mol
Surface area6300 Å2
MethodPISA
3
C: Guanine nucleotide exchange factor VAV2
F: Thioredoxin-interacting protein


Theoretical massNumber of molelcules
Total (without water)15,1987
Polymers15,1982
Non-polymers05
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-8 kcal/mol
Surface area6440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.764, 99.764, 160.946
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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


Mass: 13758.438 Da / Num. of mol.: 3 / Fragment: UNP residues 667-782
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV2 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-V2R-pRARE2 / References: UniProt: P52735
#2: Protein/peptide Thioredoxin-interacting protein / Thioredoxin-binding protein 2 / Vitamin D3 up-regulated protein 1


Mass: 1439.568 Da / Num. of mol.: 3 / Fragment: UNP residues 327-338 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H3M7
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 14 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30% PEG550-MME, 0.1 M ammonium sulfate, 0.1 M cacodylate pH 6.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→38.06 Å / Num. obs: 35154 / % possible obs: 99.9 % / Redundancy: 20.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.9
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique all% possible all
1.95-220.93.950334240799.4
8.94-38.0615.360.3697145698.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
Aimless0.2.17data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BMB

1bmb


Resolution: 1.95→38.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.2043 / WRfactor Rwork: 0.1712 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8393 / SU B: 6.342 / SU ML: 0.1 / SU R Cruickshank DPI: 0.1356 / SU Rfree: 0.1283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. JLIGAND WAS USED TO PREPARE RESTRAINTS FOR THE AMIDE TERMINUS OF THE PEPTIDE. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS ...Details: ARP/WARP WAS USED FOR AUTOMATED MODEL BUILDING. JLIGAND WAS USED TO PREPARE RESTRAINTS FOR THE AMIDE TERMINUS OF THE PEPTIDE. COOT WAS USED FOR INTERACTIVE MODEL BUILDING. MODEL GEOMETRY WAS EVALUATED WITH MOLPROBITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 997 2.8 %THIN SHELLS (SFTOOLS)
Rwork0.1862 ---
obs0.1871 35076 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.5 Å2 / Biso mean: 34.3927 Å2 / Biso min: 17.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 14 145 2903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192939
X-RAY DIFFRACTIONr_bond_other_d0.0020.022660
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9574000
X-RAY DIFFRACTIONr_angle_other_deg0.86636147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5975353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62524.698149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76615496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.5981512
X-RAY DIFFRACTIONr_chiral_restr0.1040.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023314
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02694
X-RAY DIFFRACTIONr_mcbond_it2.3281.8861378
X-RAY DIFFRACTIONr_mcbond_other2.3171.8831377
X-RAY DIFFRACTIONr_mcangle_it3.4182.7951725
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 127 -
Rwork0.219 2391 -
all-2518 -
obs--98.98 %
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)
14.50971.0305-2.4823.5321-0.52466.7412-0.08780.0689-0.1497-0.0592-0.0763-0.19360.1660.09220.16410.0455-0.04620.0150.0663-0.00360.02183.269215.507611.4813
23.9475-1.33941.20874.7128-1.29135.6051-0.0881-0.0790.0912-0.02990.0226-0.2402-0.08120.29370.06550.07950.0903-0.02310.1356-0.030.022284.902544.9715-12.8994
34.73410.77321.97173.18261.40475.3388-0.08590.04260.11440.0887-0.0002-0.0788-0.1079-0.05010.08610.0322-0.03960.00450.0682-0.01940.0129104.924836.372414.3309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A667 - 769
2X-RAY DIFFRACTION2B667 - 769
3X-RAY DIFFRACTION3C667 - 769

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