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- PDB-1doa: Structure of the rho family gtp-binding protein cdc42 in complex ... -

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Basic information

Entry
Database: PDB / ID: 1doa
TitleStructure of the rho family gtp-binding protein cdc42 in complex with the multifunctional regulator rhogdi
Components
  • PROTEIN (GDP-DISSOCIATION INHIBITOR 1)
  • PROTEIN (GTP-BINDING PROTEIN)
KeywordsCELL CYCLE / GTP-binding protein / Cdc42 / RhoGDI
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / 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 ...Rho GDP-dissociation inhibitor activity / 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 / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / RHOU GTPase cycle / Rho protein signal transduction / macrophage differentiation / immunological synapse / 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 / GTPase activator activity / 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
Similarity search - Function
Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Cdc42 / Coagulation Factor XIII; Chain A, domain 1 / Small GTPase Rho / small GTPase Rho family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...Coagulation Factor XIII, subunit A, domain 1 / Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Cdc42 / Coagulation Factor XIII; Chain A, domain 1 / 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 / Distorted Sandwich / Small GTP-binding protein domain / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GERAN-8-YL GERAN / Rho GDP-dissociation inhibitor 1 / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsHoffman, G.R. / Nassar, N. / Cerione, R.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI.
Authors: Hoffman, G.R. / Nassar, N. / Cerione, R.A.
History
DepositionDec 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GTP-BINDING PROTEIN)
B: PROTEIN (GDP-DISSOCIATION INHIBITOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6546
Polymers45,8882
Non-polymers7664
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-29 kcal/mol
Surface area20880 Å2
MethodPISA
2
A: PROTEIN (GTP-BINDING PROTEIN)
B: PROTEIN (GDP-DISSOCIATION INHIBITOR 1)
hetero molecules

A: PROTEIN (GTP-BINDING PROTEIN)
B: PROTEIN (GDP-DISSOCIATION INHIBITOR 1)
hetero molecules

A: PROTEIN (GTP-BINDING PROTEIN)
B: PROTEIN (GDP-DISSOCIATION INHIBITOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,96318
Polymers137,6646
Non-polymers2,29912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
Buried area18270 Å2
ΔGint-117 kcal/mol
Surface area59490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.940, 83.940, 191.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-200-

MG

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein PROTEIN (GTP-BINDING PROTEIN) / CDC42


Mass: 21254.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): SF9 CELLS / Production host: unidentified baculovirus / References: UniProt: P60953
#2: Protein PROTEIN (GDP-DISSOCIATION INHIBITOR 1) / RHO GDI 1


Mass: 24633.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Plasmid: PGEX-KG / Production host: Escherichia coli (E. coli) / References: UniProt: P19803

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Non-polymers , 4 types, 54 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15% PEG 4000, 100 mM Glutamic Acid, 25 mM MgSO4, 50 mM Tris, 2 mM NaN3, 2 mM LDAO , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 18K, temperature 291K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
215-20 %PEG40001reservoir
325 mM1reservoirMgSO4
4100 mMglutamic acid1reservoir
52 mMlauryldimethylamine-oxide1reservoir
6100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 39.9 Å / Num. obs: 15454 / % possible obs: 100 % / Redundancy: 5.9 % / Num. measured all: 90533 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.64 Å / % possible obs: 99.8 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementResolution: 2.6→39.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1370695.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1563 10.1 %RANDOM
Rwork0.257 ---
obs0.257 15437 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.02 Å2 / ksol: 0.203 e/Å3
Displacement parametersBiso mean: 77.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.49 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 50 50 3201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.461 241 9.3 %
Rwork0.457 2344 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP_UPPSALA.PARGDP_UPPSALA.TOP
X-RAY DIFFRACTION3CARB.PARCARB.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER.PARAMWATER.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 75.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.64
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28
LS refinement shell
*PLUS
Rfactor Rfree: 0.48 / Rfactor Rwork: 0.471

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