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- PDB-5jhh: Crystal structure of the ternary complex between the human RhoA, ... -

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Basic information

Entry
Database: PDB / ID: 5jhh
TitleCrystal structure of the ternary complex between the human RhoA, its inhibitor and the DH/PH domain of human ARHGEF11
Components
  • Rho guanine nucleotide exchange factor 11
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN/TRANSCRIPTION/INHIBITOR / RhoA-inhibitor-ARHGEF11 ternary complex / target-based pharmaceutical design / SIGNALING PROTEIN-TRANSCRIPTION-INHIBITOR complex
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 / regulation of osteoblast proliferation ...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 / regulation of osteoblast proliferation / 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 / forebrain radial glial cell differentiation / cell junction assembly / apical junction assembly / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / RHO GTPases Activate ROCKs / regulation of modification of postsynaptic structure / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / odontogenesis / PCP/CE pathway / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / regulation of small GTPase mediated signal transduction / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / positive regulation of leukocyte adhesion to vascular endothelial cell / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / NRAGE signals death through JNK / RHOB GTPase cycle / myosin binding / establishment of cell polarity / EPHA-mediated growth cone collapse / stress fiber assembly / positive regulation of cytokinesis / regulation of neuron projection development / RHOC GTPase cycle / cellular response to cytokine stimulus / androgen receptor signaling pathway / cerebral cortex cell migration / ERBB2 Regulates Cell Motility / cleavage furrow / Rho protein signal transduction / semaphorin-plexin signaling pathway / CDC42 GTPase cycle / ficolin-1-rich granule membrane / mitotic spindle assembly / endothelial cell migration / RHOA GTPase cycle / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / striated muscle contraction / cytoplasmic microtubule organization / negative regulation of reactive oxygen species biosynthetic process / RHO GTPases activate PKNs / skeletal muscle tissue development / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / substantia nigra development / positive regulation of neuron differentiation / RAC1 GTPase cycle / regulation of cell migration / cell-matrix adhesion / GTPase activator activity / substrate adhesion-dependent cell spreading / secretory granule membrane / small monomeric GTPase / kidney development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / guanyl-nucleotide exchange factor activity / cell periphery / regulation of cell growth / regulation of actin cytoskeleton organization / G protein-coupled receptor binding
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 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. / PDZ domain / 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 / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / 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
Chem-RA0 / Rho guanine nucleotide exchange factor 11 / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLv, Z. / Wang, R. / Ma, L. / Miao, Q. / Wu, J. / Yan, Z. / Li, J. / Miao, L. / Wang, F.
Funding support China, 1items
OrganizationGrant numberCountry
Jiangsu Province science and technology plan items (Jiangsu Province science and technology enterprise technology innovation Fund)BC2013062 China
CitationJournal: To Be Published
Title: Crystallization and preliminary X-ray crystallographic analysis of a small GTPase RhoA bound with its inhibitor and PDZRhoGEF
Authors: Wang, R. / Yan, Z. / Lv, Z. / Ma, L. / Miao, Q. / Chen, Q. / Wang, F. / Li, J. / Miao, L.
History
DepositionApr 21, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6679
Polymers126,7504
Non-polymers9175
Water8,611478
1
A: Rho guanine nucleotide exchange factor 11
B: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8805
Polymers63,3752
Non-polymers5053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-4 kcal/mol
Surface area25230 Å2
MethodPISA
2
E: Rho guanine nucleotide exchange factor 11
F: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7884
Polymers63,3752
Non-polymers4122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-10 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.855, 119.049, 90.526
Angle α, β, γ (deg.)90.00, 114.39, 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: 42907.656 Da / Num. of mol.: 2 / Fragment: UNP residues 714-1081
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Production host: Escherichia Coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O15085
#2: Protein Transforming protein RhoA / Rho cDNA clone 12 / h12


Mass: 20467.457 Da / Num. of mol.: 2 / Fragment: UNP residues 1-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARH12, ARHA, RHO12 / Production host: Escherichia Coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-RA0 / 3-{3-[ethyl(quinolin-2-yl)amino]phenyl}propanoic acid


Mass: 320.385 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H20N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2% v/v Tacsimate pH 5.0, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.541782 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541782 Å / Relative weight: 1
ReflectionResolution: 2.3→82.44 Å / Num. obs: 73383 / % possible obs: 96.3 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 19.268
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.7 / % possible all: 93.2

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Processing

SoftwareName: REFMAC / Version: 5.8.0073 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→82.44 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 6.56 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.207 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23904 3565 4.9 %RANDOM
Rwork0.1932 ---
obs0.1955 69765 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.03 Å2
2---0.04 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.3→82.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8675 0 66 478 9219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0199064
X-RAY DIFFRACTIONr_bond_other_d0.0020.028940
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.98612238
X-RAY DIFFRACTIONr_angle_other_deg0.8143.00120600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8551097
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49623.959437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.478151755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6381585
X-RAY DIFFRACTIONr_chiral_restr0.10.21366
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022022
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4463.8224358
X-RAY DIFFRACTIONr_mcbond_other3.443.8214357
X-RAY DIFFRACTIONr_mcangle_it5.135.7115465
X-RAY DIFFRACTIONr_mcangle_other5.1315.7125466
X-RAY DIFFRACTIONr_scbond_it4.4934.3764706
X-RAY DIFFRACTIONr_scbond_other4.4934.3774707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0286.3446774
X-RAY DIFFRACTIONr_long_range_B_refined9.7230.64610838
X-RAY DIFFRACTIONr_long_range_B_other9.7230.65410839
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 255 -
Rwork0.262 4872 -
obs--91.41 %

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