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- PDB-3msx: Crystal structure of RhoA.GDP.MgF3 in complex with GAP domain of ... -

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Basic information

Entry
Database: PDB / ID: 3msx
TitleCrystal structure of RhoA.GDP.MgF3 in complex with GAP domain of ArhGAP20
Components
  • Rho GTPase-activating protein 20
  • Transforming protein RhoA
KeywordsPROTEIN BINDING / protein-proten complex / transition state / GTPase
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity ...alpha-beta T cell lineage commitment / aortic valve formation / mitotic cleavage furrow formation / positive regulation of lipase activity / bone trabecula morphogenesis / endothelial tube lumen extension / skeletal muscle satellite cell migration / positive regulation of vascular associated smooth muscle contraction / angiotensin-mediated vasoconstriction involved in regulation of systemic arterial blood pressure / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / negative regulation of intracellular steroid hormone receptor signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / regulation of neural precursor cell proliferation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / regulation of Rho protein signal transduction / apical junction assembly / cell junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / establishment of epithelial cell apical/basal polarity / beta selection / regulation of systemic arterial blood pressure by endothelin / negative regulation of cell size / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / positive regulation of podosome assembly / regulation of small GTPase mediated signal transduction / apolipoprotein A-I-mediated signaling pathway / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / positive regulation of leukocyte adhesion to vascular endothelial cell / wound healing, spreading of cells / motor neuron apoptotic process / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / EPHA-mediated growth cone collapse / myosin binding / regulation of neuron projection development / stress fiber assembly / cellular response to cytokine stimulus / RHOC GTPase cycle / positive regulation of cytokinesis / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / androgen receptor signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOA GTPase cycle / mitotic spindle assembly / negative regulation of cell-substrate adhesion / Rho protein signal transduction / positive regulation of protein serine/threonine kinase activity / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / RHO GTPases activate PKNs / GPVI-mediated activation cascade / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / cytoplasmic microtubule organization / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / GTPase activator activity / regulation of cell migration / secretory granule membrane / small monomeric GTPase / cell-matrix adhesion / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell morphogenesis / cytoplasmic side of plasma membrane / VEGFA-VEGFR2 Pathway
Similarity search - Function
: / : / : / Rho GTPase-activating protein 20, PH domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Rho GTPase-activating protein domain ...: / : / : / Rho GTPase-activating protein 20, PH domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / 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 / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily / 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
GUANOSINE-5'-DIPHOSPHATE / TRIFLUOROMAGNESATE / Transforming protein RhoA / Rho GTPase-activating protein 20
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsUtepbergenov, D. / Cooper, D.R. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: To be Published
Title: Mechanism of molecular specificity of RhoGAP domains towards small GTPases of RhoA family.
Authors: Utepbergenov, D. / Cooper, D.R. / Derewenda, U. / Somlyo, A.V. / Derewenda, Z.S.
History
DepositionApr 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming protein RhoA
B: Rho GTPase-activating protein 20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4915
Polymers42,9422
Non-polymers5493
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-26 kcal/mol
Surface area16370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.057, 88.977, 137.725
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-84-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20363.309 Da / Num. of mol.: 1 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARH12, ARHA, RHO12, RHOA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: P61586, small monomeric GTPase
#2: Protein Rho GTPase-activating protein 20 / Rho-type GTPase-activating protein 20


Mass: 22578.984 Da / Num. of mol.: 1 / Fragment: GAP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGAP20, KIAA1391 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIPL / References: UniProt: Q9P2F6

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Non-polymers , 4 types, 225 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris, pH 8.5, 100 mM NaCl, 5 mM NaF, 5 mM MgCl2, 5mM 2-mercaptoethanol and 20 w/v% PEG 8000, 0.2 M NaCl, 0.17 M NH4Cl, 0.1 ...Details: Crystallization drop was 1:1 mixture of protein dissolved in 20 mM Tris, pH 8.5, 100 mM NaCl, 5 mM NaF, 5 mM MgCl2, 5mM 2-mercaptoethanol and 20 w/v% PEG 8000, 0.2 M NaCl, 0.17 M NH4Cl, 0.1 M phosphate citrate buffer. The crystallization reservoir was 20 w/v% PEG 8000, 0.2 M NaCl, 0.17 M NH4Cl, 0.1 M phosphate citrate buffer, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97166 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 4, 2008
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97166 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 41890 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.061 / Χ2: 1.08 / Net I/σ(I): 12.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.65-1.6897.30.128581.131100
3.11-3.237.30.1018621.077100
3.23-3.387.40.0888611.118100
3.38-3.567.40.0748741.162100
3.56-3.787.30.0648751.185100
3.78-4.077.30.0548761.03100
4.07-4.487.30.0478730.983100
4.48-5.137.20.0439051.033100
5.13-6.4670.0568851.05899.9
6.46-406.60.0559531.0299.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→27.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.848 / SU B: 4.599 / SU ML: 0.076 / SU R Cruickshank DPI: 0.162 / SU Rfree: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2229 5.1 %RANDOM
Rwork0.195 ---
obs0.196 41890 85.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.87 Å2 / Biso mean: 37.867 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 33 222 3184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223031
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9874112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1165369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38325.035141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69415540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2321517
X-RAY DIFFRACTIONr_chiral_restr0.0940.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022271
X-RAY DIFFRACTIONr_nbd_refined0.2180.21392
X-RAY DIFFRACTIONr_nbtor_refined0.310.22129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.212
X-RAY DIFFRACTIONr_mcbond_it2.3441.51899
X-RAY DIFFRACTIONr_mcangle_it2.89523009
X-RAY DIFFRACTIONr_scbond_it4.87231272
X-RAY DIFFRACTIONr_scangle_it5.7974.51102
LS refinement shellResolution: 1.65→1.689 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 80 -
Rwork0.269 1537 -
all-1617 -
obs--43.33 %

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