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- PDB-6bc1: A Complex between PH Domain of p190RhoGEF and Activated Rac1 Boun... -

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Basic information

Entry
Database: PDB / ID: 6bc1
TitleA Complex between PH Domain of p190RhoGEF and Activated Rac1 Bound to a GTP Analog
Components
  • Ras-related C3 botulinum toxin substrate 1
  • Rho guanine nucleotide exchange factor 28
KeywordsSIGNALING PROTEIN / Rho GTPase Guanine Nucleotide Exchange Factors RhoGEF Pleckstrin Homology PH domain
Function / homology
Function and homology information


regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 ...regulation of respiratory burst / negative regulation of interleukin-23 production / regulation of neutrophil migration / localization within membrane / Activated NTRK2 signals through CDK5 / NADPH oxidase complex / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / cortical cytoskeleton organization / respiratory burst / hepatocyte growth factor receptor signaling pathway / regulation of Rho protein signal transduction / ruffle organization / cell projection assembly / thioesterase binding / negative regulation of fibroblast migration / regulation of stress fiber assembly / RHO GTPases activate CIT / Nef and signal transduction / sphingosine-1-phosphate receptor signaling pathway / PCP/CE pathway / motor neuron axon guidance / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / regulation of lamellipodium assembly / positive regulation of neutrophil chemotaxis / Azathioprine ADME / Activation of RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / MET activates RAP1 and RAC1 / Wnt signaling pathway, planar cell polarity pathway / regulation of small GTPase mediated signal transduction / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / lamellipodium assembly / positive regulation of Rho protein signal transduction / establishment or maintenance of cell polarity / regulation of cell size / DSCAM interactions / Activation of RAC1 downstream of NMDARs / RHOB GTPase cycle / Rho GDP-dissociation inhibitor binding / small GTPase-mediated signal transduction / NRAGE signals death through JNK / Rac protein signal transduction / RHOC GTPase cycle / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / Sema3A PAK dependent Axon repulsion / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate NADPH Oxidases / RHOA GTPase cycle / RHO GTPases Activate WASPs and WAVEs / anatomical structure morphogenesis / RHO GTPases activate IQGAPs / ephrin receptor signaling pathway / localization / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of lamellipodium assembly / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / RAC1 GTPase cycle / EPHB-mediated forward signaling / actin filament polymerization / cell chemotaxis / substrate adhesion-dependent cell spreading / guanyl-nucleotide exchange factor activity / cell-matrix adhesion / small monomeric GTPase / G protein activity / positive regulation of endothelial cell migration / secretory granule membrane / VEGFR2 mediated vascular permeability / Signal transduction by L1 / actin filament organization / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / MAPK6/MAPK4 signaling / trans-Golgi network / cell morphogenesis / Signaling by SCF-KIT
Similarity search - Function
ARHGEF28, PH domain / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain ...ARHGEF28, PH domain / ARHGEF1-like, PH domain / PH domain / Small GTPase Rho / small GTPase Rho family profile. / Phorbol esters/diacylglycerol binding domain (C1 domain) / 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. / 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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C1-like domain superfamily / 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 / Ras-related C3 botulinum toxin substrate 1 / Rho guanine nucleotide exchange factor 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChen, Z. / Sternweis, P.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-5R01GM031954 United States
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Direct regulation of p190RhoGEF by activated Rho and Rac GTPases.
Authors: Dada, O. / Gutowski, S. / Brautigam, C.A. / Chen, Z. / Sternweis, P.C.
History
DepositionOct 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 29, 2020Group: Derived calculations / Category: pdbx_struct_assembly_gen / Item: _pdbx_struct_assembly_gen.asym_id_list
Revision 1.6Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Ras-related C3 botulinum toxin substrate 1
C: Rho guanine nucleotide exchange factor 28
B: Ras-related C3 botulinum toxin substrate 1
D: Rho guanine nucleotide exchange factor 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2058
Polymers76,0774
Non-polymers1,1274
Water2,036113
1
A: Ras-related C3 botulinum toxin substrate 1
C: Rho guanine nucleotide exchange factor 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6024
Polymers38,0392
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related C3 botulinum toxin substrate 1
D: Rho guanine nucleotide exchange factor 28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6024
Polymers38,0392
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.332, 96.333, 189.361
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 Ras-related C3 botulinum toxin substrate 1 / Cell migration-inducing gene 5 protein / Ras-like protein TC25 / p21-Rac1


Mass: 20505.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAC1, TC25, MIG5 / Plasmid: pGEX-kG-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63000
#2: Protein Rho guanine nucleotide exchange factor 28 / 190 kDa guanine nucleotide exchange factor / p190RhoGEF / Rho guanine nucleotide exchange factor


Mass: 17533.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF28, KIAA1998, RGNEF / Plasmid: pGEX-kG-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8N1W1
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 22% PEG 3350, 100mM NaHEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.54→48.166 Å / Num. obs: 28012 / % possible obs: 99.4 % / Redundancy: 10 % / Biso Wilson estimate: 48.6 Å2 / Rsym value: 0.14 / Net I/σ(I): 16.2
Reflection shellRedundancy: 7.4 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1279 / Rsym value: 0.75 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→48.166 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3226 959 5.01 %
Rwork0.2775 --
obs0.2798 19160 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→48.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 66 113 5265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035254
X-RAY DIFFRACTIONf_angle_d0.5847124
X-RAY DIFFRACTIONf_dihedral_angle_d12.1043192
X-RAY DIFFRACTIONf_chiral_restr0.042806
X-RAY DIFFRACTIONf_plane_restr0.003888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.05290.42351350.35442561X-RAY DIFFRACTION100
3.0529-3.24410.40631350.30522551X-RAY DIFFRACTION100
3.2441-3.49450.31751340.29392550X-RAY DIFFRACTION100
3.4945-3.84610.33591350.27682564X-RAY DIFFRACTION100
3.8461-4.40230.36721370.25532584X-RAY DIFFRACTION100
4.4023-5.54510.26531380.25242630X-RAY DIFFRACTION100
5.5451-48.17310.25921450.27062761X-RAY DIFFRACTION100

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