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- PDB-6bcb: A Complex between PH Domain of p114RhoGEF and Activated RhoA Boun... -

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Basic information

Entry
Database: PDB / ID: 6bcb
TitleA Complex between PH Domain of p114RhoGEF and Activated RhoA Bound to a GTP Analog
Components
  • Rho guanine nucleotide exchange factor 18
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / Rho GTPase Guanine Nucleotide Exchange Factors RhoGEF Pleckstrin Homology PH domain
Function / homology
Function and homology information


: / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / NRAGE signals death through JNK / protein localization to cell-cell junction / G alpha (12/13) signalling events / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity ...: / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / NRAGE signals death through JNK / protein localization to cell-cell junction / G alpha (12/13) signalling events / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / positive regulation of lipase activity / 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 / regulation of neural precursor cell proliferation / cleavage furrow formation / regulation of modification of postsynaptic actin cytoskeleton / regulation of osteoblast proliferation / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / regulation of systemic arterial blood pressure by endothelin / regulation of Rho protein signal transduction / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / beta selection / establishment of epithelial cell apical/basal polarity / regulation of modification of postsynaptic structure / negative regulation of cell size / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / motor neuron apoptotic process / wound healing, spreading of cells / PI3K/AKT activation / positive regulation of leukocyte adhesion to vascular endothelial cell / negative regulation of stress fiber assembly / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / small GTPase-mediated signal transduction / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / androgen receptor signaling pathway / positive regulation of cytokinesis / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / Rho protein signal transduction / ficolin-1-rich granule membrane / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / cytoplasmic microtubule organization / regulation of microtubule cytoskeleton organization / skeletal muscle tissue development / negative regulation of reactive oxygen species biosynthetic process / regulation of cell migration / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / cell-matrix adhesion / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / secretory granule membrane / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization
Similarity search - Function
ARHGEF18, PH domain / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. ...ARHGEF18, PH domain / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family profile. / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Transforming protein RhoA / Rho guanine nucleotide exchange factor 18
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.401 Å
AuthorsSternweis, P.C. / Chen, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-5R01GM031954 United States
CitationJournal: Data Brief / Year: 2018
Title: Crystal structures of the PH domains from Lbc family of RhoGEFs bound to activated RhoA GTPase.
Authors: Chen, Z. / Gutowski, S. / Sternweis, P.C.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Transforming protein RhoA
A: Rho guanine nucleotide exchange factor 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2725
Polymers37,6462
Non-polymers6263
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-25 kcal/mol
Surface area16560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.934, 60.039, 65.475
Angle α, β, γ (deg.)90.00, 108.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules FA

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


Mass: 20865.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Plasmid: pGEX-kG-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#2: Protein Rho guanine nucleotide exchange factor 18


Mass: 16780.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Arhgef18, Kiaa0521 / Plasmid: pGEX-kG-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6P9R4

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Non-polymers , 4 types, 434 molecules

#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 22-24% PEG 3350, 100mM Bis-Tris, 200mM NaCl / PH range: 5.8-6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2012
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.4→27.291 Å / Num. obs: 70421 / % possible obs: 99.6 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.3 Å2 / Rsym value: 0.06 / Net I/σ(I): 23.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 3332 / Rsym value: 0.56 / % possible all: 95.1

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.401→27.291 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1649 3520 5 %
Rwork0.1362 --
obs0.1377 70380 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.401→27.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2594 0 37 431 3062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012686
X-RAY DIFFRACTIONf_angle_d1.3433627
X-RAY DIFFRACTIONf_dihedral_angle_d12.9361039
X-RAY DIFFRACTIONf_chiral_restr0.071401
X-RAY DIFFRACTIONf_plane_restr0.007462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4006-1.41980.25231230.20352366X-RAY DIFFRACTION89
1.4198-1.44010.25931410.18482625X-RAY DIFFRACTION97
1.4401-1.46160.2451400.1732613X-RAY DIFFRACTION98
1.4616-1.48450.19571370.1672706X-RAY DIFFRACTION99
1.4845-1.50880.20461390.15622611X-RAY DIFFRACTION100
1.5088-1.53480.19531390.14112703X-RAY DIFFRACTION100
1.5348-1.56270.19151380.13532653X-RAY DIFFRACTION100
1.5627-1.59280.15751540.12722713X-RAY DIFFRACTION100
1.5928-1.62530.17611380.12632688X-RAY DIFFRACTION100
1.6253-1.66060.1721410.12282652X-RAY DIFFRACTION100
1.6606-1.69920.17081410.12392690X-RAY DIFFRACTION100
1.6992-1.74170.15561400.11752688X-RAY DIFFRACTION100
1.7417-1.78880.16521560.12562667X-RAY DIFFRACTION100
1.7888-1.84140.15071300.11932699X-RAY DIFFRACTION100
1.8414-1.90080.15361430.11782705X-RAY DIFFRACTION100
1.9008-1.96880.14611400.12312682X-RAY DIFFRACTION100
1.9688-2.04760.16261470.11882691X-RAY DIFFRACTION100
2.0476-2.14070.15431300.12042706X-RAY DIFFRACTION100
2.1407-2.25350.14871480.11862682X-RAY DIFFRACTION100
2.2535-2.39460.14661460.12482700X-RAY DIFFRACTION100
2.3946-2.57940.18531360.12982717X-RAY DIFFRACTION100
2.5794-2.83870.15111430.13742706X-RAY DIFFRACTION100
2.8387-3.24890.16271480.14482702X-RAY DIFFRACTION100
3.2489-4.09110.13741330.14062737X-RAY DIFFRACTION100
4.0911-27.29620.18031490.15672758X-RAY DIFFRACTION100

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