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- PDB-2qrz: Cdc42 bound to GMP-PCP: Induced Fit by Effector is Required -

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Basic information

Entry
Database: PDB / ID: 2qrz
TitleCdc42 bound to GMP-PCP: Induced Fit by Effector is Required
ComponentsCell division control protein 42 homolog precursor
KeywordsCELL CYCLE / G-domain fold / G protein / GTPase / Alternative splicing / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Prenylation
Function / homology
Function and homology information


GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / 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 ...GBD domain binding / submandibular salivary gland formation / actin filament branching / Golgi transport complex / 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 / 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 / establishment or maintenance of cell polarity / phagocytosis, engulfment / RHOV GTPase cycle / 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 / macrophage differentiation / RHOG GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RAC2 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / filopodium / secretory granule / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / EGFR downregulation / positive regulation of JNK cascade / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / protein localization / G beta:gamma signalling through CDC42 / cytoplasmic ribonucleoprotein granule / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / cellular response to type II interferon / endocytosis / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity
Similarity search - Function
Cdc42 / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...Cdc42 / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsPhillips, M.J. / Calero, G. / Chan, B. / Cerione, R.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Effector Proteins Exert an Important Influence on the Signaling-active State of the Small GTPase Cdc42.
Authors: Phillips, M.J. / Calero, G. / Chan, B. / Ramachandran, S. / Cerione, R.A.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: 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: Cell division control protein 42 homolog precursor
B: Cell division control protein 42 homolog precursor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3027
Polymers42,1152
Non-polymers1,1875
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-50.2 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.500, 98.500, 102.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Cell division control protein 42 homolog precursor


Mass: 21057.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Cdc42 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P60953
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#5: 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: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 6K, 100 mM Na Acetate, 50 mM MES, pH 6.0, 100 mM Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→31.27 Å / Num. obs: 20185 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.8
Reflection shellHighest resolution: 2.4 Å / Num. measured all: 2959

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→31.27 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1438867.625 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1034 5.1 %RANDOM
Rwork0.234 ---
obs-20185 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.815 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 72.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å20 Å2
2--2.35 Å20 Å2
3----4.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→31.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2931 0 71 115 3117
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d3.05
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.438 180 5.4 %
Rwork0.377 3124 -
all-3304 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gmppcp.pargmppcp.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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