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- PDB-1xcg: Crystal Structure of Human RhoA in complex with DH/PH fragment of... -

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Basic information

Entry
Database: PDB / ID: 1xcg
TitleCrystal Structure of Human RhoA in complex with DH/PH fragment of PDZRHOGEF
Components
  • Rho guanine nucleotide exchange factor 11
  • Transforming protein RhoA
KeywordsSIGNALING PROTEIN ACTIVATOR/SIGNALING PROTEIN / X-ray crystallography / regulation of RhoA GTPase / protein complex / SIGNALING PROTEIN ACTIVATOR-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


alpha-beta T cell lineage commitment / aortic valve formation / 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 / bone trabecula morphogenesis / RHO GTPases Activate Rhotekin and Rhophilins ...alpha-beta T cell lineage commitment / aortic valve formation / 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 / bone trabecula morphogenesis / 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 osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / forebrain radial glial cell differentiation / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / cell junction assembly / beta selection / establishment of epithelial cell apical/basal polarity / cellular response to chemokine / negative regulation of motor neuron apoptotic process / regulation of systemic arterial blood pressure by endothelin / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / negative regulation of cell size / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / regulation of small GTPase mediated signal transduction / positive regulation of alpha-beta T cell differentiation / positive regulation of podosome assembly / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / motor neuron apoptotic process / Wnt signaling pathway, planar cell polarity pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / odontogenesis / PI3K/AKT activation / ossification involved in bone maturation / regulation of focal adhesion assembly / androgen receptor signaling pathway / negative chemotaxis / RHOB GTPase cycle / EPHA-mediated growth cone collapse / NRAGE signals death through JNK / apical junction complex / stress fiber assembly / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / regulation of neuron projection development / cellular response to cytokine stimulus / establishment of cell polarity / cerebral cortex cell migration / positive regulation of protein serine/threonine kinase activity / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / cleavage furrow / CDC42 GTPase cycle / ficolin-1-rich granule membrane / negative regulation of cell-substrate adhesion / RHOA GTPase cycle / mitotic spindle assembly / positive regulation of T cell migration / endothelial cell migration / skeletal muscle tissue development / Rho protein signal transduction / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / GPVI-mediated activation cascade / striated muscle contraction / negative regulation of reactive oxygen species biosynthetic process / positive regulation of stress fiber assembly / RAC1 GTPase cycle / cytoplasmic microtubule organization / EPHB-mediated forward signaling / substrate adhesion-dependent cell spreading / positive regulation of neuron differentiation / substantia nigra development / guanyl-nucleotide exchange factor activity / regulation of cell migration / secretory granule membrane / cell-matrix adhesion / regulation of microtubule cytoskeleton organization / GTPase activator activity / small monomeric GTPase / cell periphery / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of actin cytoskeleton organization / kidney development / regulation of cell growth
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 / PDZ superfamily / 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 / 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 / MAD / Resolution: 2.5 Å
AuthorsDerewenda, U. / Oleksy, A. / Stevenson, A.S. / Korczynska, J. / Dauter, Z. / Somlyo, A.P. / Otlewski, J. / Somlyo, A.V. / Derewenda, Z.S.
CitationJournal: Structure / Year: 2004
Title: The crystal structure of RhoA in complex with the DH/PH fragment of PDZRhoGEF, an activator of the Ca(2+) sensitization pathway in smooth muscle
Authors: Derewenda, U. / Oleksy, A. / Stevenson, A.S. / Korczynska, J. / Dauter, Z. / Somlyo, A.P. / Otlewski, J. / Somlyo, A.V. / Derewenda, Z.S.
History
DepositionSep 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)125,8754
Polymers125,8754
Non-polymers00
Water1,63991
1
A: Rho guanine nucleotide exchange factor 11
B: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,9382
Polymers62,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-5 kcal/mol
Surface area25960 Å2
MethodPISA
2
E: Rho guanine nucleotide exchange factor 11
F: Transforming protein RhoA


Theoretical massNumber of molelcules
Total (without water)62,9382
Polymers62,9382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-6 kcal/mol
Surface area25870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.236, 118.782, 90.130
Angle α, β, γ (deg.)90.00, 114.34, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21E
12B
22F
13A
23E

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNARGARGAA714 - 9321 - 219
21GLNGLNARGARGEC714 - 9321 - 219
12ALAALAGLNGLNBB3 - 1801 - 178
22ALAALAGLNGLNFD3 - 1801 - 178
13LEULEUALAALAAA933 - 1081220 - 368
23LEULEUALAALAEC933 - 1081220 - 368

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 42776.465 Da / Num. of mol.: 2 / Fragment: DH/PH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARHGEF11, KIAA0380 / Production host: Escherichia coli (E. coli) / References: UniProt: O15085
#2: Protein Transforming protein RhoA / H12


Mass: 20161.037 Da / Num. of mol.: 2 / Fragment: RhoA / Mutation: F25N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RHOA, ARHA, ARH12, RHO12 / Production host: Escherichia coli (E. coli) / References: UniProt: P61586
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.2
Details: PEG, Hepes, pH 7.2, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction
IDCrystal-ID
11
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9B10.979
SYNCHROTRONNSLS X9B20.97919
SYNCHROTRONNSLS X9B30.97178
SYNCHROTRONAPS 19-ID41
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMADMx-ray1
2GRAPHITESINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979191
30.971781
411
ReflectionResolution: 2.5→25 Å / Num. all: 57314 / Num. obs: 57314 / % possible obs: 96.83 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHELXDphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.935 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2899 -Random
Rwork0.224 ---
all0.235 57314 --
obs0.235 57314 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.948 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å2-1.12 Å2
2---4.59 Å20 Å2
3---3 Å2
Refine analyzeLuzzati coordinate error obs: 0.372 Å
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8659 0 0 91 8750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218802
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.97411866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6751063
X-RAY DIFFRACTIONr_chiral_restr0.0620.21345
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026520
X-RAY DIFFRACTIONr_nbd_refined0.2140.23913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.29
X-RAY DIFFRACTIONr_mcbond_it0.4921.55351
X-RAY DIFFRACTIONr_mcangle_it0.9728672
X-RAY DIFFRACTIONr_scbond_it1.58333451
X-RAY DIFFRACTIONr_scangle_it2.6824.53194
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1821loose positional0.385
2B1411loose positional0.415
3A1085loose positional0.725
1A1821loose thermal1.9210
2B1411loose thermal1.5110
3A1085loose thermal1.8310
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.333 3740
obs-3740

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