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- PDB-3t06: Crystal Structure of the DH/PH fragment of PDZRHOGEF with N-termi... -

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Basic information

Entry
Database: PDB / ID: 3t06
TitleCrystal Structure of the DH/PH fragment of PDZRHOGEF with N-terminal regulatory elements in complex with Human RhoA
Components
  • Rho guanine nucleotide exchange factor 11
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / DH-PH RhoA complex / PDZRhoGEF / GUANINE NUCLEOTIDE EXCHANGE FACTOR / RhoA
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 / apical junction assembly / regulation of modification of postsynaptic structure / 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 oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / negative regulation of cell size / 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 / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / Wnt signaling pathway, planar cell polarity pathway / odontogenesis / motor neuron apoptotic process / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / apical junction complex / RHOB GTPase cycle / EPHA-mediated growth cone collapse / NRAGE signals death through JNK / stress fiber assembly / positive regulation of cytokinesis / androgen receptor signaling pathway / establishment of cell polarity / myosin binding / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / positive regulation of protein serine/threonine kinase activity / mitotic spindle assembly / RHOA GTPase cycle / negative regulation of cell-substrate adhesion / positive regulation of T cell migration / endothelial cell migration / striated muscle contraction / Rho protein signal transduction / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / skeletal muscle tissue development / GPVI-mediated activation cascade / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of neuron differentiation / substrate adhesion-dependent cell spreading / GTPase activator activity / regulation of microtubule cytoskeleton organization / regulation of cell migration / guanyl-nucleotide exchange factor activity / secretory granule membrane / cell-matrix adhesion / small monomeric GTPase / cell periphery / regulation of actin cytoskeleton organization / regulation of cell growth / kidney development
Similarity search - Function
Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / RGS domain / RGS domain profile. ...Rho guanine nucleotide exchange factor 11, PH domain / Rho guanine nucleotide exchange factor 11, RGS domain / Regulator of G protein signalling-like domain / Regulator of G protein signalling-like domain / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / ARHGEF1-like, PH domain / PH domain / RGS domain / RGS domain profile. / Regulator of G protein signalling domain / RGS, subdomain 2 / RGS domain superfamily / Small GTPase Rho / Small GTPase Rho domain 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. / PDZ domain / Pleckstrin homology domain. / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Rho guanine nucleotide exchange factor 11 / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsBielnicki, J.A. / Derewenda, U. / Derewenda, Z.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Insights into the Molecular Activation Mechanism of the RhoA-specific Guanine Nucleotide Exchange Factor, PDZRhoGEF.
Authors: Bielnicki, J.A. / Shkumatov, A.V. / Derewenda, U. / Somlyo, A.V. / Svergun, D.I. / Derewenda, Z.S.
History
DepositionJul 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references
Revision 1.2Oct 19, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rho guanine nucleotide exchange factor 11
B: Transforming protein RhoA
E: Rho guanine nucleotide exchange factor 11
F: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)137,2484
Polymers137,2484
Non-polymers00
Water00
1
A: Rho guanine nucleotide exchange factor 11
B: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)68,6242
Polymers68,6242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-6 kcal/mol
Surface area25610 Å2
MethodPISA
2
E: Rho guanine nucleotide exchange factor 11
F: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)68,6242
Polymers68,6242
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-6 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.370, 118.630, 92.443
Angle α, β, γ (deg.)90.00, 113.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Rho guanine nucleotide exchange factor 11 / PDZ-RhoGEF


Mass: 48462.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Plasmid: pDEST15 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15085
#2: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20161.037 Da / Num. of mol.: 2 / 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) / References: UniProt: P61586

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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: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15 M DL-malic acid, 20 % w/v PEG 3350, pH 7.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 12.02 / Number: 135276 / Rmerge(I) obs: 0.097 / Χ2: 1.01 / D res high: 2.84 Å / D res low: 30 Å / Num. obs: 36903 / % possible obs: 93.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.693099.710.0590.9953.8
6.127.6910010.071.0463.9
5.366.1299.910.0780.983.9
4.875.3610010.0721.0073.9
4.524.8710010.0681.0474
4.254.5210010.0741.0614
4.044.2510010.0820.9464
3.874.0410010.0941.0064
3.723.8799.910.1111.0574
3.593.7299.910.1311.0864
3.483.5999.810.1671.0444
3.383.4810010.1991.0753.9
3.293.3899.710.2520.9563.9
3.213.2999.210.2950.9613.7
3.143.2196.910.3180.9963.4
3.073.1491.710.330.9983.2
3.013.0783.610.3490.9933
2.953.0175.710.3890.9722.7
2.92.9567.810.3931.0012.5
2.852.959.110.3960.952.3
ReflectionResolution: 2.84→30 Å / Num. all: 39384 / Num. obs: 36903 / % possible obs: 93.7 % / Observed criterion σ(I): -4 / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.84-2.92.30.396159.1
2.9-2.952.50.393167.8
2.95-3.012.70.389175.7
3.01-3.0730.349183.6
3.07-3.143.20.33191.7
3.14-3.213.40.318196.9
3.21-3.293.70.295199.2
3.29-3.383.90.252199.7
3.38-3.483.90.1991100
3.48-3.5940.167199.8
3.59-3.7240.131199.9
3.72-3.8740.111199.9
3.87-4.0440.0941100
4.04-4.2540.0821100
4.25-4.5240.0741100
4.52-4.8740.0681100
4.87-5.363.90.0721100
5.36-6.123.90.078199.9
6.12-7.693.90.071100
7.69-303.80.059199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_818refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XCG

1xcg


Resolution: 2.84→29.824 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.9 / σ(F): 1.35 / Phase error: 29.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2572 1849 5.01 %
Rwork0.2077 --
obs0.2102 36871 93.55 %
all-39434 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.425 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.465 Å20 Å2-12.3514 Å2
2---11.4003 Å20 Å2
3----5.0647 Å2
Refinement stepCycle: LAST / Resolution: 2.84→29.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8657 0 0 0 8657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018802
X-RAY DIFFRACTIONf_angle_d1.26511870
X-RAY DIFFRACTIONf_dihedral_angle_d19.7843440
X-RAY DIFFRACTIONf_chiral_restr0.081345
X-RAY DIFFRACTIONf_plane_restr0.0051534
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.84-2.9170.3543950.30521705X-RAY DIFFRACTION60
2.917-3.00270.39621170.29642129X-RAY DIFFRACTION74
3.0027-3.09960.31311380.28092461X-RAY DIFFRACTION87
3.0996-3.21020.3261620.25932754X-RAY DIFFRACTION96
3.2102-3.33860.36691430.25732856X-RAY DIFFRACTION99
3.3386-3.49030.30351590.23122866X-RAY DIFFRACTION100
3.4903-3.6740.2981380.22312890X-RAY DIFFRACTION100
3.674-3.90370.26541400.20492870X-RAY DIFFRACTION100
3.9037-4.20440.24771270.19842926X-RAY DIFFRACTION100
4.2044-4.62610.24111580.16882869X-RAY DIFFRACTION100
4.6261-5.29230.22381450.16792884X-RAY DIFFRACTION100
5.2923-6.65550.26081560.24172902X-RAY DIFFRACTION100
6.6555-29.82560.17571710.16962910X-RAY DIFFRACTION100

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