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- PDB-5c2k: Crystal structure of the fusion protein linked by RhoA and the GA... -

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Basic information

Entry
Database: PDB / ID: 5c2k
TitleCrystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP
ComponentsTransforming protein RhoA,Rac GTPase-activating protein 1
KeywordsHYDROLASE ACTIVATOR / GTPase activation / fusion protein / small G protein
Function / homology
Function and homology information


centralspindlin complex / actomyosin contractile ring assembly / mitotic spindle midzone assembly / sulfate transmembrane transport / neuroblast proliferation / regulation of attachment of spindle microtubules to kinetochore / alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity ...centralspindlin complex / actomyosin contractile ring assembly / mitotic spindle midzone assembly / sulfate transmembrane transport / neuroblast proliferation / regulation of attachment of spindle microtubules to kinetochore / alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / negative regulation of oxidative phosphorylation / Flemming body / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / gamma-tubulin binding / RHO GTPases activate CIT / RHOD GTPase cycle / odontogenesis / regulation of small GTPase mediated signal transduction / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / Kinesins / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / stress fiber assembly / positive regulation of leukocyte adhesion to vascular endothelial cell / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / regulation of focal adhesion assembly / ossification involved in bone maturation / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / COPI-dependent Golgi-to-ER retrograde traffic / RHOB GTPase cycle / EPHA-mediated growth cone collapse / apical junction complex / myosin binding / positive regulation of cytokinesis / spindle midzone / RHOC GTPase cycle / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / phosphatidylinositol-3,4,5-trisphosphate binding / mitotic cytokinesis / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / ficolin-1-rich granule membrane / mitotic spindle assembly / RAC3 GTPase cycle / Rho protein signal transduction / RHOA GTPase cycle / RAC2 GTPase cycle / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / monoatomic ion transport / positive regulation of neuron differentiation / alpha-tubulin binding / GPVI-mediated activation cascade / beta-tubulin binding / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / RAC1 GTPase cycle / EPHB-mediated forward signaling / regulation of cell migration / MHC class II antigen presentation / substantia nigra development / acrosomal vesicle / regulation of embryonic development / erythrocyte differentiation / secretory granule membrane / regulation of actin cytoskeleton organization / cell periphery / GTPase activator activity
Similarity search - Function
Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / 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 domain profile. / Rho GTPase activation protein / Phorbol esters/diacylglycerol binding domain (C1 domain) ...Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / 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 domain 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 / Transforming protein RhoA / Rac GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.3Dec 4, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
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 / _pdbx_entry_details.has_protein_modification
Revision 1.4Aug 12, 2026Group: Advisory / Derived calculations
Category: pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere ...pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Description: Metalloprotein remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA,Rac GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6224
Polymers46,0711
Non-polymers5513
Water10,971609
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-18 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.491, 77.041, 62.253
Angle α, β, γ (deg.)90.00, 108.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transforming protein RhoA,Rac GTPase-activating protein 1 / MgcRacGAP


Mass: 46070.906 Da / Num. of mol.: 1 / Fragment: GAP domain, UNP residues 346-546 / Mutation: S249D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, RACGAP1 / Plasmid: pCR2.1 / Production host: Cell-free synthesis (others) / References: UniProt: P61586, UniProt: Q9H0H5
#2: Chemical ChemComp-MG / MAGNESIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
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: 2.2 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: PEG3350, Bis-Tris

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.42→50 Å / Num. obs: 73586 / % possible obs: 99.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 16.5 Å2 / Net I/σ(I): 21.9
Reflection shellResolution: 1.42→1.47 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.47 / % possible all: 94.7

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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 , 1TX4

2ovj

1tx4


Resolution: 1.42→32.26 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 975869.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3754 5.1 %RANDOM
Rwork0.184 ---
obs0.184 73566 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.9972 Å2 / ksol: 0.378865 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-6.27 Å20 Å2-1.62 Å2
2---2.73 Å20 Å2
3----3.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.13 Å
Refinement stepCycle: 1 / Resolution: 1.42→32.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2952 1811 33 609 5405
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.5
X-RAY DIFFRACTIONc_mcangle_it1.532
X-RAY DIFFRACTIONc_scbond_it1.972
X-RAY DIFFRACTIONc_scangle_it2.942.5
LS refinement shellResolution: 1.42→1.51 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 594 5.3 %
Rwork0.248 10680 -
obs--90.5 %
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 DIFFRACTION4GDP.paramGDP.top
X-RAY DIFFRACTION5af3.paramaf3.top

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