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- PDB-1a4r: G12V MUTANT OF HUMAN PLACENTAL CDC42 GTPASE IN THE GDP FORM -

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Basic information

Entry
Database: PDB / ID: 1a4r
TitleG12V MUTANT OF HUMAN PLACENTAL CDC42 GTPASE IN THE GDP FORM
ComponentsG25K GTP-BINDING PROTEIN
KeywordsHYDROLASE / GTPASE / SIGNAL TRANSDUCTION
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 / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / neuron fate determination / modulation by host of viral process / GTP-dependent protein binding / organelle transport along microtubule / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / cardiac conduction system development / Inactivation of CDC42 and RAC1 / establishment of Golgi localization / leading edge membrane / regulation of filopodium assembly / neuropilin signaling pathway / positive regulation of intracellular protein transport / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / mitogen-activated protein kinase kinase kinase binding / regulation of modification of postsynaptic structure / dendritic spine morphogenesis / embryonic heart tube development / thioesterase binding / regulation of stress fiber assembly / RHO GTPases activate KTN1 / nuclear migration / regulation of lamellipodium assembly / adherens junction organization / sprouting angiogenesis / DCC mediated attractive signaling / Wnt signaling pathway, planar cell polarity pathway / CD28 dependent Vav1 pathway / positive regulation of filopodium assembly / regulation of postsynapse organization / regulation of mitotic nuclear division / RHOV GTPase cycle / establishment or maintenance of cell polarity / phagocytosis, engulfment / heart contraction / positive regulation of DNA replication / 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 / RAC2 GTPase cycle / RHO GTPases Activate WASPs and WAVEs / RAC3 GTPase cycle / RHO GTPases activate IQGAPs / spindle midzone / negative regulation of protein-containing complex assembly / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / phagocytic vesicle / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / EGFR downregulation / small monomeric GTPase / G protein activity / secretory granule / filopodium / actin filament organization / integrin-mediated signaling pathway / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCGR3A-mediated phagocytosis / MAPK6/MAPK4 signaling / Schaffer collateral - CA1 synapse / G beta:gamma signalling through CDC42 / mitotic spindle / Regulation of actin dynamics for phagocytic cup formation / cellular response to type II interferon / VEGFA-VEGFR2 Pathway / cytoplasmic ribonucleoprotein granule / endocytosis / positive regulation of neuron apoptotic process / ubiquitin protein ligase activity / cell-cell junction
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / AMINOPHOSPHONIC ACID-GUANYLATE ESTER / Cell division control protein 42 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRudolph, M.G. / Vetter, I.R. / Wittinghofer, A.
CitationJournal: Protein Sci. / Year: 1999
Title: Nucleotide binding to the G12V-mutant of Cdc42 investigated by X-ray diffraction and fluorescence spectroscopy: two different nucleotide states in one crystal.
Authors: Rudolph, M.G. / Wittinghofer, A. / Vetter, I.R.
History
DepositionFeb 2, 1998Processing site: BNL
Revision 1.0Mar 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G25K GTP-BINDING PROTEIN
B: G25K GTP-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5615
Polymers42,6512
Non-polymers9103
Water97354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.650, 98.650, 104.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.5633, 0.8245, -0.0532), (0.8231, -0.5656, -0.0511), (-0.0722, -0.015, -0.9973)
Vector: 2.4698, -4.0516, 6.267)

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Components

#1: Protein G25K GTP-BINDING PROTEIN / G25K / CDC42 HOMOLOG


Mass: 21325.660 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA / Cell line: BL21 / Cellular location: CYTOPLASM, INNER SIDE OF MEMBRANE / Plasmid: PGEX2T / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P60953
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-GNH / AMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 442.216 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N6O10P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.9 Å3/Da / Density % sol: 51 %
Crystal growpH: 4.6 / Details: pH 4.60
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 mMprotein1drop
220 mMHEPES-NaOH1drop
31 mM1dropMgCl2
40.1 M1reservoirNaOAc
55 %PEG40001reservoir
60.3 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.0774
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0774 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 17611 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 46.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.6
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / Num. obs: 18254 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Num. measured all: 88071
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q21 WITH ALL NON-CONSERVED RESIDUES MUTATED TO ALANINE

4q21


Resolution: 2.5→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1738 9.9 %RANDOM
Rwork0.228 ---
obs0.228 17611 95.9 %-
Displacement parametersBiso mean: 57.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3087 0 29 54 3170
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.67
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.041.5
X-RAY DIFFRACTIONx_mcangle_it4.842
X-RAY DIFFRACTIONx_scbond_it4.742
X-RAY DIFFRACTIONx_scangle_it6.982.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.5→2.54 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 74 9 %
Rwork0.38 746 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOP
X-RAY DIFFRACTION3MG.PARMG.TOP
X-RAY DIFFRACTION4GDP.PARGDP.TOP
X-RAY DIFFRACTION5GPN.PARGPN.TOP
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.225 / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.67
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / Rfactor Rwork: 0.38

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