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- PDB-1kzg: DbsCdc42(Y889F) -

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Basic information

Entry
Database: PDB / ID: 1kzg
TitleDbsCdc42(Y889F)
Components
  • CDC42 HOMOLOG
  • GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
KeywordsSIGNALING PROTEIN / guanine nucleotide exchange factor / small G-protein / Cdc42 / Dbs / DH/PH
Function / homology
Function and homology information


RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / 1-phosphatidylinositol binding / NRAGE signals death through JNK / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle ...RHOB GTPase cycle / RHOC GTPase cycle / CDC42 GTPase cycle / RHOA GTPase cycle / 1-phosphatidylinositol binding / NRAGE signals death through JNK / GBD domain binding / submandibular salivary gland formation / actin filament branching / RAC1 GTPase cycle / Golgi transport complex / RHOG GTPase cycle / positive regulation of pinocytosis / modification of synaptic structure / endothelin receptor signaling pathway involved in heart process / Cdc42 protein signal transduction / cardiac neural crest cell migration involved in outflow tract morphogenesis / positive regulation of synapse structural plasticity / dendritic cell migration / G alpha (12/13) signalling events / storage vacuole / apolipoprotein A-I receptor binding / positive regulation of epithelial cell proliferation involved in lung morphogenesis / neuron fate determination / modulation by host of viral process / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / Inactivation of CDC42 and RAC1 / cardiac conduction system development / GTP-dependent protein binding / regulation of filopodium assembly / establishment of Golgi localization / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / mitogen-activated protein kinase kinase kinase binding / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / regulation of lamellipodium assembly / nuclear migration / DCC mediated attractive signaling / adherens junction organization / sprouting angiogenesis / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / regulation of postsynapse organization / positive regulation of filopodium assembly / regulation of mitotic nuclear division / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / extrinsic component of membrane / heart contraction / Myogenesis / RHOJ GTPase cycle / Golgi organization / RHOQ GTPase cycle / positive regulation of cytokinesis / RHO GTPases activate PAKs / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / endomembrane system / positive regulation of DNA replication / negative regulation of protein-containing complex assembly / phagocytic vesicle / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / substantia nigra development / extrinsic component of cytoplasmic side of plasma membrane / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / filopodium / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins
Similarity search - Function
DBS, SH3 domain / DBS, PH domain / Cdc42 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) ...DBS, SH3 domain / DBS, PH domain / Cdc42 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Divergent CRAL/TRIO domain / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / Small GTPase Rho / small GTPase Rho family 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 42 homolog / Guanine nucleotide exchange factor DBS
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRossman, K.L. / Worthylake, D.K. / Snyder, J.T. / Siderovski, D.P. / Campbell, S.L. / Sondek, J.
CitationJournal: EMBO J. / Year: 2002
Title: A crystallographic view of interactions between Dbs and Cdc42: PH domain-assisted guanine nucleotide exchange.
Authors: Rossman, K.L. / Worthylake, D.K. / Snyder, J.T. / Siderovski, D.P. / Campbell, S.L. / Sondek, J.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
B: CDC42 HOMOLOG
C: GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
D: CDC42 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)124,3574
Polymers124,3574
Non-polymers00
Water2,072115
1
A: GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
B: CDC42 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)62,1782
Polymers62,1782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-14 kcal/mol
Surface area25870 Å2
MethodPISA
2
C: GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS
D: CDC42 HOMOLOG


Theoretical massNumber of molelcules
Total (without water)62,1782
Polymers62,1782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-15 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.320, 88.190, 232.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GUANINE NUCLEOTIDE EXCHANGE FACTOR DBS / DBL'S BIG SISTER / DBS


Mass: 41236.332 Da / Num. of mol.: 2 / Fragment: DH/PH fragment (residues 623-967) / Mutation: Y889F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dbs / Plasmid: pET-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q64096
#2: Protein CDC42 HOMOLOG / G25K GTP-BINDING PROTEIN


Mass: 20942.070 Da / Num. of mol.: 2 / Fragment: residues 1-188 / Mutation: C188S
Source method: isolated from a genetically manipulated source
Details: PLACENTAL ISOFORM / Source: (gene. exp.) Homo sapiens (human) / Gene: Cdc42 / Plasmid: pET-21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P60953
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000,Tris HCL, NaFormate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
114 mg/mlprotein1drop
210 mMTris1droppH8.0
325 mM1dropNaCl
42 mMdithiothreitol1drop
51 mMEDTA1drop
650 mMTris1reservoirpH7.0
712 %PEG80001reservoir
8650 mMsodium formate1reservoir
92 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 15, 2001
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→31.16 Å / Num. all: 43383 / Num. obs: 43383 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 50.8 Å2 / Limit h max: 25 / Limit h min: 0 / Limit k max: 33 / Limit k min: 0 / Limit l max: 89 / Limit l min: 0 / Observed criterion F max: 1800892.67 / Observed criterion F min: 9.2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 99.7
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 50 Å / Num. obs: 43434 / % possible obs: 99.6 % / Num. measured all: 225476 / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Dbs/Cdc42 (1KZ7)

1kz7


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2169 5 %random
Rwork0.217 ---
all-41214 --
obs-41214 99.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 41.2991 Å2 / ksol: 0.359355 e/Å3
Displacement parametersBiso max: 146.06 Å2 / Biso mean: 57.73 Å2 / Biso min: 16.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å20 Å20 Å2
2--2.32 Å20 Å2
3----5.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.38 Å
Luzzati d res high-2.6
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8281 0 0 115 8396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg22.2
X-RAY DIFFRACTIONx_torsion_impr_deg0.8
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.6-2.720.3132574.80.31650440.025331530199.4
2.72-2.860.2952514.70.29851000.0195371535199.6
2.86-3.040.272504.70.27151090.0175374535999.7
3.04-3.270.2562494.60.25551190.0165376536899.8
3.27-3.60.2482845.30.24650900.0155392537499.7
3.6-4.120.212915.30.20851470.0125447543899.8
4.12-5.170.1792875.20.17851950.0115497548299.7
5.17-200.1832965.20.18553320.0115688562898.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 20 Å / Rfactor obs: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.29
LS refinement shell
*PLUS
Rfactor obs: 0.316

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