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- PDB-3ky9: Autoinhibited Vav1 -

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Basic information

Entry
Database: PDB / ID: 3ky9
TitleAutoinhibited Vav1
ComponentsProto-oncogene vav
KeywordsAPOPTOSIS / VAV1 / CALPONIN HOMOLOGY DOMAIN / DBL HOMOLOGY DOMAIN / PLECKSTRIN HOMOLOGY DOMAIN / C1 DOMAIN / Guanine-nucleotide releasing factor / Metal-binding / Phosphoprotein / Proto-oncogene / SH2 domain / SH3 domain / Zinc-finger
Function / homology
Function and homology information


phosphorylation-dependent protein binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of cell size / regulation of GTPase activity / NRAGE signals death through JNK / positive regulation of natural killer cell mediated cytotoxicity / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway ...phosphorylation-dependent protein binding / Azathioprine ADME / regulation of small GTPase mediated signal transduction / CD28 dependent Vav1 pathway / regulation of cell size / regulation of GTPase activity / NRAGE signals death through JNK / positive regulation of natural killer cell mediated cytotoxicity / Fc-gamma receptor signaling pathway involved in phagocytosis / Fc-epsilon receptor signaling pathway / RHOG GTPase cycle / T cell differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / RHOA GTPase cycle / RAC2 GTPase cycle / vascular endothelial growth factor receptor signaling pathway / Erythropoietin activates RAS / GPVI-mediated activation cascade / RAC1 GTPase cycle / T cell costimulation / reactive oxygen species metabolic process / phosphotyrosine residue binding / FCERI mediated Ca+2 mobilization / guanyl-nucleotide exchange factor activity / neutrophil chemotaxis / VEGFR2 mediated vascular permeability / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / integrin-mediated signaling pathway / Regulation of signaling by CBL / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Signaling by SCF-KIT / Regulation of actin dynamics for phagocytic cup formation / platelet activation / VEGFA-VEGFR2 Pathway / Constitutive Signaling by Aberrant PI3K in Cancer / G alpha (12/13) signalling events / cell-cell junction / cell migration / cellular response to xenobiotic stimulus / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Potential therapeutics for SARS / intracellular signal transduction / immune response / G protein-coupled receptor signaling pathway / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain ...VAV1 protein, second SH3 domain / VAV1 protein, first SH3 domain / VAV1, SH2 domain / Vav, PH domain / Smooth muscle protein/calponin / Calmodulin-regulated spectrin-associated protein-like, Calponin-homology domain / CAMSAP CH domain / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 / 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. / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 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 / Roll / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / MAD / Resolution: 2.731 Å
AuthorsTomchick, D.R. / Rosen, M.K. / Machius, M. / Yu, B.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2010
Title: Structural and Energetic Mechanisms of Cooperative Autoinhibition and Activation of Vav1
Authors: Yu, B. / Martins, I.R. / Li, P. / Amarasinghe, G.K. / Umetani, J. / Fernandez-Zapico, M.E. / Billadeau, D.D. / Machius, M. / Tomchick, D.R. / Rosen, M.K.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Internal dynamics control activation and activity of the autoinhibited Vav DH domain
Authors: Li, P. / Martins, I.R. / Amarasinghe, G.K. / Rosen, M.K.
#2: Journal: Biochemistry / Year: 2005
Title: Acidic region tyrosines provide access points for allosteric activation of the autoinhibited Vav1 Dbl homology domain.
Authors: Amarasinghe, G.K. / Rosen, M.K.
#3: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structural basis for relief of autoinhibition of the Dbl homology domain of proto-oncogene Vav by tyrosine phosphorylation.
Authors: Aghazadeh, B. / Lowry, W.E. / Huang, X.Y. / Rosen, M.K.
History
DepositionDec 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proto-oncogene vav
B: Proto-oncogene vav
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,6696
Polymers137,4072
Non-polymers2624
Water0
1
A: Proto-oncogene vav
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8343
Polymers68,7041
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Proto-oncogene vav
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8343
Polymers68,7041
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.376, 58.738, 160.721
Angle α, β, γ (deg.)90.00, 97.31, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 2:129 or resseq 156:180 or resseq...
211chain B and (resseq 2:129 or resseq 156:180 or resseq...

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.987013, -0.004843, 0.160568), (-0.004231, 0.999982, 0.00415), (-0.160585, 0.003417, -0.987016)19.0271, 24.520901, 83.911697

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Components

#1: Protein Proto-oncogene vav


Mass: 68703.523 Da / Num. of mol.: 2 / Fragment: CH-DH-PH-C1 DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VAV, VAV1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)TI / References: UniProt: P15498
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M TRIS, 0.05 M NACL, 5% GLYCEROL, 2 mM TCEP, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.28317 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 15, 2007 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28317 Å / Relative weight: 1
ReflectionResolution: 2.73→47.3 Å / Num. all: 42421 / Num. obs: 42421 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 72.455 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 44.8
Reflection shellResolution: 2.73→2.78 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.959 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MLPHAREphasing
DMphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.731→47.286 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.95 / Isotropic thermal model: ISOTROPIC PLUS TLS / σ(F): 1.33 / Phase error: 29.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2705 1683 4.05 %
Rwork0.2234 --
obs0.2254 41518 97.63 %
all-41518 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.827 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso mean: 112.701 Å2
Baniso -1Baniso -2Baniso -3
1--20.254 Å2-0 Å2-1.769 Å2
2---18.797 Å20 Å2
3----15.684 Å2
Refinement stepCycle: LAST / Resolution: 2.731→47.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8809 0 4 0 8813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088972
X-RAY DIFFRACTIONf_angle_d1.1512059
X-RAY DIFFRACTIONf_dihedral_angle_d17.8793395
X-RAY DIFFRACTIONf_chiral_restr0.0821301
X-RAY DIFFRACTIONf_plane_restr0.0041567
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A4273X-RAY DIFFRACTIONPOSITIONAL
12B4273X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.731-2.81140.35761000.29562439X-RAY DIFFRACTION72
2.8114-2.90210.34351300.29483362X-RAY DIFFRACTION100
2.9021-3.00580.33491450.26933346X-RAY DIFFRACTION100
3.0058-3.12610.29241370.25873413X-RAY DIFFRACTION100
3.1261-3.26840.34141270.26043396X-RAY DIFFRACTION100
3.2684-3.44070.32181450.25383362X-RAY DIFFRACTION100
3.4407-3.65610.29631450.24323389X-RAY DIFFRACTION100
3.6561-3.93830.26461620.21173368X-RAY DIFFRACTION100
3.9383-4.33440.24431450.19083390X-RAY DIFFRACTION100
4.3344-4.9610.24471360.18193429X-RAY DIFFRACTION100
4.961-6.24810.25351390.2093435X-RAY DIFFRACTION100
6.2481-47.29270.21471720.19283506X-RAY DIFFRACTION99
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)
10.8889-2.0939-0.60441.02790.29730.2442-0.4130.6106-1.09640.45220.04950.54871.45491.04870.51361.1459-0.12230.43860.6552-0.28770.8737-5.4252-3.874424.8454
22.7245-0.7066-1.30692.37190.46932.6324-0.75851.6437-0.49570.00530.12891.15610.1228-1.56830.57010.3025-0.29670.20081.0571-0.30190.7449-15.28796.533521.3522
30.0340.7892-0.96130.5252-0.58461.3291-0.3921-0.2452-0.42730.3065-0.1113-0.07490.6411-0.11870.22480.63580.07430.0160.46440.030.63334.873213.721819.4222
42.2428-0.1089-3.44550.3939-0.11222.66861.36541.02250.4596-0.7552-0.7278-0.2936-1.225-0.485-0.53470.93610.30380.14120.65830.12510.392311.867732.96554.503
53.8895-0.921-2.85511.09640.71495.93430.76920.77980.2046-0.1037-0.3967-0.1107-1.5316-0.8411-0.34830.67540.15580.02660.32720.03980.33857.41133.791110.6613
61.2887-0.18580.13780.0926-0.89541.0494-0.5127-0.2898-0.81330.46310.05480.106-0.5461-0.13350.23830.5851-0.0385-0.1050.25440.10310.526513.326928.915925.5159
72.45550.5567-1.40421.9453-0.00950.76850.03580.04880.39181.46040.07410.6123-0.9874-0.5359-0.310.98780.49340.43190.54510.16460.5902-17.972923.74643.5131
81.16390.1507-1.27291.1267-0.48870.15930.5246-0.87250.48961.8865-0.01350.0467-1.69310.6749-0.34631.7613-0.11990.0130.8013-0.17910.6222.606439.635541.3974
90.36710.6961-0.60511.2398-2.832.2910.0502-0.2478-0.6679-0.4470.10360.12231.0694-0.3199-0.03190.67440.03440.1360.52830.20210.634533.9367-28.855354.2483
102.96990.0466-1.18172.7612-0.54871.7463-0.384-0.8075-0.05160.0930.2416-0.4835-0.06680.59630.20490.22340.19660.05470.56430.12940.48643.9916-17.690556.3079
112.1534.1575.01510.6772-1.85164.35271.18830.8006-1.9106-0.38431.1026-1.4348-0.64370.1123-1.77280.82620.21620.22671.2978-0.31160.798546.5843-33.556746.3063
12-0.3939-1.0633-0.61943.61781.59855.6357-0.7782-0.07610.02980.13230.20230.89010.3512-0.00210.60960.75080.0282-0.16650.6879-0.10920.816732.7218-14.990751.9839
134.45251.2046-2.97252.7583-1.92568.49740.5865-0.618-0.03980.4425-0.46540.5146-1.30110.2172-0.15340.6073-0.01580.02920.5494-0.01960.467821.83037.620872.2373
140.0198-0.05970.11330.7190.16911.1312-0.17290.9958-0.5298-1.0718-0.04750.7079-0.2843-1.0621-0.03720.48050.031-0.18670.80860.10430.878812.05674.249757.074
152.3001-0.8651-0.96233.33750.40011.6833-0.10410.20570.2144-0.4397-0.1385-0.3398-0.07490.46270.11780.5762-0.23560.1020.60740.03470.480142.4291-0.878433.8603
161.2812-0.02290.25940.9126-0.73110.9578-0.18390.0015-0.0920.16690.20690.1525-0.0877-0.33240.05320.5604-0.0727-0.18750.48350.09140.425922.929815.141539.3533
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:28)
2X-RAY DIFFRACTION2(chain A and resid 29:142)
3X-RAY DIFFRACTION3(chain A and resid 143:194)
4X-RAY DIFFRACTION4(chain A and resid 195:226)
5X-RAY DIFFRACTION5(chain A and resid 227:351)
6X-RAY DIFFRACTION6(chain A and resid 352:378)
7X-RAY DIFFRACTION7(chain A and resid 379:499)
8X-RAY DIFFRACTION8(chain A and resid 500:564)
9X-RAY DIFFRACTION9(chain B and resid 1:28)
10X-RAY DIFFRACTION10(chain B and resid 29:128)
11X-RAY DIFFRACTION11(chain B and resid 129:142)
12X-RAY DIFFRACTION12(chain B and resid 143:171)
13X-RAY DIFFRACTION13(chain B and resid 172:349)
14X-RAY DIFFRACTION14(chain B and resid 350:376)
15X-RAY DIFFRACTION15(chain B and resid 377:499)
16X-RAY DIFFRACTION16(chain B and resid 500:565)

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