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- PDB-5jcp: RhoGAP domain of ARAP3 in complex with RhoA in the transition state -

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Basic information

Entry
Database: PDB / ID: 5jcp
TitleRhoGAP domain of ARAP3 in complex with RhoA in the transition state
ComponentsArf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA
KeywordsSIGNALING PROTEIN / HYDROLASE / RhoA / RhoGAP / ARAP3
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 modification of postsynaptic structure / cell junction assembly / apical 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 oxidative phosphorylation / negative regulation of motor neuron apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / RHO GTPases activate CIT / RHO GTPases Activate ROCKs / negative regulation of cell size / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / positive regulation of podosome assembly / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / apolipoprotein A-I-mediated signaling pathway / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / stress fiber assembly / androgen receptor signaling pathway / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / phosphatidylinositol-3,4,5-trisphosphate binding / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / cleavage furrow / CDC42 GTPase cycle / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / mitotic spindle assembly / RAC3 GTPase cycle / positive regulation of T cell migration / endothelial cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / GPVI-mediated activation cascade / Rho protein signal transduction / RHO GTPases activate PKNs / vesicle-mediated transport / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / ruffle / cytoplasmic microtubule organization / RAC1 GTPase cycle / EPHB-mediated forward signaling / cytoskeleton organization / positive regulation of neuron differentiation / substantia nigra development / substrate adhesion-dependent cell spreading / regulation of microtubule cytoskeleton organization / regulation of cell migration / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / cell periphery / regulation of actin cytoskeleton organization / kidney development / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction
Similarity search - Function
ARAP, RhoGAP domain / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger ...ARAP, RhoGAP domain / : / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / 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 domain profile. / Rho GTPase activation protein / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / PH domain / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / 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
TETRAFLUOROALUMINATE ION / GUANOSINE-5'-DIPHOSPHATE / Transforming protein RhoA / Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBao, H. / Li, F. / Wang, C. / Wang, N. / Jiang, Y. / Tang, Y. / Wu, J. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for the Specific Recognition of RhoA by the Dual GTPase-activating Protein ARAP3
Authors: Bao, H. / Li, F. / Wang, C. / Wang, N. / Jiang, Y. / Tang, Y. / Wu, J. / Shi, Y.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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 / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA
A: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4068
Polymers94,2652
Non-polymers1,1416
Water3,459192
1
B: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7034
Polymers47,1331
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-14 kcal/mol
Surface area16120 Å2
MethodPISA
2
A: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7034
Polymers47,1331
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-14 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.786, 93.208, 164.283
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA


Mass: 47132.617 Da / Num. of mol.: 2 / Fragment: UNP residues 906-1107,UNP residues 2-181 / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) synthetic construct (others)
Gene: ARAP3, RHOA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8WWN8, UniProt: P61586
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.31 Å3/Da / Density % sol: 46.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100 mM MES, 15%(v/v) PEG 550 MME, 4%(v/v) Acetone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 52079 / % possible obs: 99.8 % / Redundancy: 6 % / Biso Wilson estimate: 30.96 Å2 / Rmerge(I) obs: 0.108 / Net I/av σ(I): 15.922 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.186.10.506199.9
2.18-2.266.10.383199.9
2.26-2.376.10.291100
2.37-2.496.10.212199.9
2.49-2.656.10.1681100
2.65-2.8560.135199.8
2.85-3.1460.12199.8
3.14-3.5960.115199.9
3.59-4.525.90.09199.8
4.52-505.70.066199.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data scaling
PHASER2.5.2phasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JD0, 1A2B

5jd0

1a2b


Resolution: 2.1→46.711 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2266 2644 5.12 %
Rwork0.1864 --
obs0.1885 51671 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→46.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5581 0 68 192 5841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075739
X-RAY DIFFRACTIONf_angle_d0.917776
X-RAY DIFFRACTIONf_dihedral_angle_d17.8163504
X-RAY DIFFRACTIONf_chiral_restr0.055884
X-RAY DIFFRACTIONf_plane_restr0.0061007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.13820.28141210.22592533X-RAY DIFFRACTION100
2.1382-2.17930.29031430.21132555X-RAY DIFFRACTION100
2.1793-2.22380.24161180.20152542X-RAY DIFFRACTION100
2.2238-2.27220.27461470.20372572X-RAY DIFFRACTION100
2.2722-2.3250.2641470.19682507X-RAY DIFFRACTION100
2.325-2.38320.24521380.18882562X-RAY DIFFRACTION100
2.3832-2.44760.23381460.18712535X-RAY DIFFRACTION100
2.4476-2.51960.25941330.19162557X-RAY DIFFRACTION100
2.5196-2.60090.27441290.19542589X-RAY DIFFRACTION100
2.6009-2.69390.25311430.20072553X-RAY DIFFRACTION100
2.6939-2.80170.26511560.20642532X-RAY DIFFRACTION100
2.8017-2.92920.23851220.21572595X-RAY DIFFRACTION100
2.9292-3.08360.24761420.21852563X-RAY DIFFRACTION100
3.0836-3.27680.22721370.20122591X-RAY DIFFRACTION100
3.2768-3.52970.25161510.19782604X-RAY DIFFRACTION100
3.5297-3.88470.19581540.17752588X-RAY DIFFRACTION100
3.8847-4.44650.1931250.15542643X-RAY DIFFRACTION100
4.4465-5.60060.21131310.15052654X-RAY DIFFRACTION100
5.6006-46.72210.18311610.18072752X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.869 Å / Origin y: -3.4692 Å / Origin z: 18.0172 Å
111213212223313233
T0.1729 Å2-0.027 Å2-0.003 Å2-0.1891 Å2-0.0339 Å2--0.2426 Å2
L0.358 °2-0.0342 °20.0387 °2-0.8498 °2-0.1459 °2--0.6714 °2
S0.0317 Å °-0.0027 Å °-0.024 Å °-0.1694 Å °0.0095 Å °0.0563 Å °-0.0326 Å °0.0601 Å °-0.0416 Å °
Refinement TLS groupSelection details: all

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