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- PDB-5c2j: Complex structure of the GAP domain of MgcRacGAP and Cdc42 -

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Basic information

Entry
Database: PDB / ID: 5c2j
TitleComplex structure of the GAP domain of MgcRacGAP and Cdc42
Components
  • Cell division control protein 42 homolog
  • Rac GTPase-activating protein 1
KeywordsHYDROLASE ACTIVATOR/SIGNALING PROTEIN / GTPase activation / Complex / small G-protein / HYDROLASE ACTIVATOR-SIGNALING PROTEIN complex
Function / homology
Function and homology information


DCC mediated attractive signaling / RHO GTPases activate KTN1 / centralspindlin complex / RHOV GTPase cycle / CD28 dependent Vav1 pathway / RHOQ GTPase cycle / RHOU GTPase cycle / RAC3 GTPase cycle / establishment or maintenance of apical/basal cell polarity / RAC2 GTPase cycle ...DCC mediated attractive signaling / RHO GTPases activate KTN1 / centralspindlin complex / RHOV GTPase cycle / CD28 dependent Vav1 pathway / RHOQ GTPase cycle / RHOU GTPase cycle / RAC3 GTPase cycle / establishment or maintenance of apical/basal cell polarity / RAC2 GTPase cycle / RHO GTPases activate PAKs / CDC42 GTPase cycle / actomyosin contractile ring assembly / G beta:gamma signalling through CDC42 / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RHO GTPases Activate WASPs and WAVEs / nucleus localization / EGFR downregulation / GBD domain binding / submandibular salivary gland formation / Golgi transport complex / positive regulation of pinocytosis / actin filament branching / RAC1 GTPase cycle / positive regulation of synapse structural plasticity / dendritic cell migration / endothelin receptor signaling pathway involved in heart process / mitotic spindle midzone assembly / sulfate transmembrane transport / cardiac neural crest cell migration involved in outflow tract morphogenesis / storage vacuole / RHO GTPases activate IQGAPs / organelle transport along microtubule / positive regulation of epithelial cell proliferation involved in lung morphogenesis / apolipoprotein A-I receptor binding / RHO GTPases Activate Formins / neuron fate determination / regulation of attachment of spindle microtubules to kinetochore / RHOG GTPase cycle / positive regulation of pseudopodium assembly / GTP-dependent protein binding / MAPK6/MAPK4 signaling / Regulation of actin dynamics for phagocytic cup formation / cardiac conduction system development / modulation by host of viral process / Factors involved in megakaryocyte development and platelet production / heart process / establishment of Golgi localization / regulation of filopodium assembly / leading edge membrane / neuropilin signaling pathway / positive regulation of intracellular protein transport / Myogenesis / cell junction assembly / filopodium assembly / establishment of epithelial cell apical/basal polarity / dendritic spine morphogenesis / VEGFA-VEGFR2 Pathway / mitogen-activated protein kinase kinase kinase binding / thioesterase binding / regulation of modification of postsynaptic structure / gamma-tubulin binding / adherens junction organization / embryonic heart tube development / RHOD GTPase cycle / Flemming body / Kinesins / regulation of small GTPase mediated signal transduction / regulation of postsynapse organization / sprouting angiogenesis / positive regulation of filopodium assembly / endosomal transport / COPI-dependent Golgi-to-ER retrograde traffic / nuclear migration / regulation of mitotic nuclear division / phagocytosis, engulfment / RHOB GTPase cycle / heart contraction / Rho GDP-dissociation inhibitor binding / establishment or maintenance of cell polarity / Golgi organization / beta-tubulin binding / RHOC GTPase cycle / cell leading edge / positive regulation of cytokinesis / phosphatidylinositol-3,4,5-trisphosphate binding / cleavage furrow / mitotic cytokinesis / lamellipodium membrane / regulation of embryonic development / CDC42 GTPase cycle / neuroblast proliferation / RHOA GTPase cycle / RAC2 GTPase cycle / alpha-tubulin binding / Rho protein signal transduction / RAC3 GTPase cycle / spindle midzone / negative regulation of protein-containing complex assembly
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Cdc42 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Small GTPase Rho / small GTPase Rho family profile. / Rho GTPase activation protein ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Cdc42 / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Small GTPase Rho / small GTPase Rho family profile. / Rho GTPase activation protein / Phorbol esters/diacylglycerol binding domain (C1 domain) / 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 / C1-like domain superfamily / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Cell division control protein 42 homolog / Rac GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Hosaka, T. / Kitamura, T. / Yokoyama, S. / Shirouzu, M.
CitationJournal: J.Struct.Biol. / Year: 2024
Title: Structural basis for the effects of Ser387 phosphorylation of MgcRacGAP on its GTPase-activating activities for CDC42 and RHOA.
Authors: Murayama, K. / Kato-Murayama, M. / Hosaka, T. / Kitamura, T. / Yokoyama, S. / Shirouzu, M.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.4Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rac GTPase-activating protein 1
B: Cell division control protein 42 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5475
Polymers44,9962
Non-polymers5513
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-15 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.324, 74.237, 55.423
Angle α, β, γ (deg.)90.00, 96.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Rac GTPase-activating protein 1 / Male germ cell RacGap / MgcRacGAP / Protein CYK4 homolog / HsCYK-4


Mass: 23192.887 Da / Num. of mol.: 1 / Fragment: GAP domain, UNP residues 346-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RACGAP1, KIAA1478, MGCRACGAP / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q9H0H5
#2: Protein Cell division control protein 42 homolog / G25K GTP-binding protein


Mass: 21803.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdc42 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: P60766

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Non-polymers , 4 types, 106 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThis sequence is based on GenBank BAA90247.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG3350, Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 12204 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 26 Å2 / Net I/σ(I): 13.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.439 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OVJ, 1GRN

2ovj

1grn


Resolution: 2.5→32.39 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 919676.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 623 5.1 %RANDOM
Rwork0.198 ---
obs0.198 12153 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.1256 Å2 / ksol: 0.3201 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-21.32 Å20 Å2-9.22 Å2
2---7.92 Å20 Å2
3----13.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.38 Å
Refinement stepCycle: 1 / Resolution: 2.5→32.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 1613 32 103 4828
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.378 98 4.9 %
Rwork0.291 1913 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR/protein_rep.paramCNS_TOPPAR/protein.top
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION3CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top
X-RAY DIFFRACTION4af3.paramaf3.top
X-RAY DIFFRACTION5GDP.paramGDP.top

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