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- PDB-3kz1: Crystal Structure of the Complex of PDZ-RhoGEF DH/PH domains with... -

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Basic information

Entry
Database: PDB / ID: 3kz1
TitleCrystal Structure of the Complex of PDZ-RhoGEF DH/PH domains with GTP-gamma-S Activated RhoA
Components
  • Rho guanine nucleotide exchange factor 11
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN / regulation of RhoA GTPase / RhoGEF / DH / PH / Rho / GTPase activation / Guanine-nucleotide releasing factor / Membrane / Cytoskeleton / GTP-binding / Magnesium / Nucleotide-binding / Prenylation / Proto-oncogene
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 / 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 / cellular response to chemokine / negative regulation of cell migration involved in sprouting angiogenesis / regulation of systemic arterial blood pressure by endothelin / establishment of epithelial cell apical/basal polarity / beta selection / 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 / PCP/CE pathway / positive regulation of podosome assembly / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / regulation of small GTPase mediated signal transduction / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / Sema4D mediated inhibition of cell attachment and migration / odontogenesis / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / wound healing, spreading of cells / positive regulation of leukocyte adhesion to vascular endothelial cell / apical junction complex / ossification involved in bone maturation / regulation of focal adhesion assembly / negative chemotaxis / RHOB GTPase cycle / myosin binding / establishment of cell polarity / EPHA-mediated growth cone collapse / NRAGE signals death through JNK / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cellular response to cytokine stimulus / 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 / endothelial cell migration / RHOA GTPase cycle / mitotic spindle assembly / 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 / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / positive regulation of neuron differentiation / substantia nigra development / RAC1 GTPase cycle / regulation of cell migration / GTPase activator activity / substrate adhesion-dependent cell spreading / cell-matrix adhesion / secretory granule membrane / small monomeric GTPase / guanyl-nucleotide exchange factor activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / regulation of cell growth / RHO GTPases Activate Formins / regulation of actin cytoskeleton organization
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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Rho guanine nucleotide exchange factor 11 / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChen, Z. / Sternweis, P.C. / Sprang, S.R.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Activated RhoA binds to the pleckstrin homology (PH) domain of PDZ-RhoGEF, a potential site for autoregulation.
Authors: Chen, Z. / Medina, F. / Liu, M.Y. / Thomas, C. / Sprang, S.R. / Sternweis, P.C.
History
DepositionDec 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Rho guanine nucleotide exchange factor 11
E: Transforming protein RhoA
F: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,3138
Polymers130,1864
Non-polymers1,1274
Water1,35175
1
A: Rho guanine nucleotide exchange factor 11
F: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6564
Polymers65,0932
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rho guanine nucleotide exchange factor 11
E: Transforming protein RhoA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6564
Polymers65,0932
Non-polymers5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.166, 111.836, 138.390
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 Rho guanine nucleotide exchange factor 11 / PDZ-RhoGEF


Mass: 44568.336 Da / Num. of mol.: 2 / Fragment: UNP residues 710-1085
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15085
#2: Protein Transforming protein RhoA / H12


Mass: 20524.510 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 / Plasmid: pGEX-kG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61586
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14-16% PEG 10000, 0.1M ammonium acetate, 0.1M Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 21, 2009 / Details: mirrors
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 38512 / % possible obs: 90.7 % / Redundancy: 4.8 % / Biso Wilson estimate: 62 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 1.46 / % possible all: 62.1

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1A2B, 1XCG

1a2b

1xcg


Resolution: 2.7→33.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / SU ML: 0.389 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.789 / ESU R Free: 0.395 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: B-factors reported represent the sum of TLS and residual B-factors
RfactorNum. reflection% reflectionSelection details
Rfree0.28328 1947 5 %RANDOM
Rwork0.23351 ---
all0.23604 ---
obs0.23604 36635 90.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 71.317 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2--2.01 Å20 Å2
3----3.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8705 0 66 75 8846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228920
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.9912044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.47551069
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94324.171422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.936151723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.581576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216576
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 100 -
Rwork0.346 1825 -
obs-1825 62.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7206-0.1355-0.88530.42930.29540.76970.04270.1642-0.132-0.0176-0.0280.0272-0.087-0.02-0.01470.3385-0.0253-0.04580.1596-0.00570.849-34.282-4.4639.978
21.7407-0.0365-0.37330.76980.6870.7374-0.048-0.11350.36990.00070.11-0.1292-0.11980.1586-0.06190.4278-0.0046-0.07230.2410.00750.9297-25.40612.54128.956
39.1573-0.2304-1.57324.1171-0.66562.96280.07450.78140.6024-0.43550.0834-0.4079-0.120.0981-0.1580.0892-0.01890.04340.1096-0.0870.938114.314-7.6210.539
47.95490.64480.62413.05580.72973.4651-0.312-0.5291.5363-0.175-0.37971.1224-0.5029-0.67950.69170.17670.1369-0.18390.1753-0.26771.4411-74.17420.19533.296
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A714 - 1082
2X-RAY DIFFRACTION1A200 - 235
3X-RAY DIFFRACTION2B715 - 1081
4X-RAY DIFFRACTION2B200 - 217
5X-RAY DIFFRACTION3E3 - 181
6X-RAY DIFFRACTION3E538 - 550
7X-RAY DIFFRACTION3E200 - 211
8X-RAY DIFFRACTION4F3 - 181
9X-RAY DIFFRACTION4F538 - 550
10X-RAY DIFFRACTION4F200 - 208

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