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- PDB-1cc0: CRYSTAL STRUCTURE OF THE RHOA.GDP-RHOGDI COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1cc0
TitleCRYSTAL STRUCTURE OF THE RHOA.GDP-RHOGDI COMPLEX
Components
  • rho GDP dissociation inhibitor alpha
  • transforming protein rhoA
KeywordsSIGNALING PROTEIN / RHO GTPASE / G-PROTEIN
Function / homology
Function and homology information


Rho GDP-dissociation inhibitor activity / alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins ...Rho GDP-dissociation inhibitor activity / alpha-beta T cell lineage commitment / aortic valve formation / beta selection / positive regulation of lipase activity / endothelial tube lumen extension / skeletal muscle satellite cell migration / bone trabecula morphogenesis / SLIT2:ROBO1 increases RHOA activity / RHO GTPases Activate Rhotekin and Rhophilins / Roundabout signaling pathway / Axonal growth inhibition (RHOA activation) / Axonal growth stimulation / cleavage furrow formation / negative regulation of cell size / regulation of osteoblast proliferation / regulation of modification of postsynaptic actin cytoskeleton / mitotic cleavage furrow formation / apical junction assembly / negative regulation of cell migration involved in sprouting angiogenesis / establishment of epithelial cell apical/basal polarity / positive regulation of alpha-beta T cell differentiation / cell junction assembly / cellular response to chemokine / regulation of Rho protein signal transduction / negative regulation of oxidative phosphorylation / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / RHO GTPases activate CIT / odontogenesis / PCP/CE pathway / Sema4D induced cell migration and growth-cone collapse / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / Sema4D mediated inhibition of cell attachment and migration / wound healing, spreading of cells / regulation of synaptic vesicle cycle / stress fiber assembly / positive regulation of leukocyte adhesion to vascular endothelial cell / Wnt signaling pathway, planar cell polarity pathway / PI3K/AKT activation / regulation of focal adhesion assembly / ossification involved in bone maturation / positive regulation of protein serine/threonine kinase activity / negative chemotaxis / EPHA-mediated growth cone collapse / apical junction complex / myosin binding / positive regulation of cytokinesis / RHOC GTPase cycle / cellular response to cytokine stimulus / ERBB2 Regulates Cell Motility / cleavage furrow / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / negative regulation of cell-substrate adhesion / RHOG GTPase cycle / immunological synapse / RHOH GTPase cycle / ficolin-1-rich granule membrane / mitotic spindle assembly / Rho protein signal transduction / RHOA GTPase cycle / RAC2 GTPase cycle / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / positive regulation of T cell migration / positive regulation of neuron differentiation / GPVI-mediated activation cascade / RHO GTPases activate PKNs / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / RAC1 GTPase cycle / EPHB-mediated forward signaling / regulation of cell migration / substantia nigra development / secretory granule membrane / regulation of actin cytoskeleton organization / cell periphery / GTPase activator activity / small monomeric GTPase / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of microtubule cytoskeleton organization / RHO GTPases Activate Formins / positive regulation of non-canonical NF-kappaB signal transduction / cell junction / VEGFA-VEGFR2 Pathway / Schaffer collateral - CA1 synapse / ruffle membrane / cytoplasmic side of plasma membrane / actin cytoskeleton organization / Ovarian tumor domain proteases / cell migration / G beta:gamma signalling through PI3Kgamma / lamellipodium / cellular response to lipopolysaccharide / G alpha (12/13) signalling events / midbody
Similarity search - Function
Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Small GTPase Rho / Small GTPase Rho domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases ...Rho protein GDP-dissociation inhibitor / Rho GDP-dissociation inhibitor domain superfamily / RHO protein GDP dissociation inhibitor / Small GTPase Rho / Small GTPase Rho domain profile. / 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 / Immunoglobulin E-set / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Rho GDP-dissociation inhibitor 1 / Transforming protein RhoA
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 5 Å
AuthorsLongenecker, K.L. / Read, P. / Derewenda, U. / Dauter, Z. / Garrard, S. / Walker, L. / Somlyo, A.V. / Somlyo, A.P. / Nakamoto, R.K. / Derewenda, Z.S.
Citation
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Crystal structure of human RhoA in a dominantly active form complexed with a GTP analogue.
Authors: Ihara, K. / Muraguchi, S. / Kato, M. / Shimizu, T. / Shirakawa, M. / Kuroda, S. / Kaibuchi, K. / Hakoshima, T.
#2: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of RhoA-GDP and its functional implications.
Authors: Wei, Y. / Zhang, Y. / Derewenda, U. / Liu, X. / Minor, W. / Nakamoto, R.K. / Somlyo, A.V. / Somlyo, A.P. / Derewenda, Z.S.
#3: Journal: Structure / Year: 1997
Title: A modulator of rho family G proteins, rhoGDI, binds these G proteins via an immunoglobulin-like domain and a flexible N-terminal arm.
Authors: Keep, N.H. / Barnes, M. / Barsukov, I. / Badii, R. / Lian, L.Y. / Segal, A.W. / Moody, P.C. / Roberts, G.C.
#4: Journal: Nature / Year: 1997
Title: C-terminal binding domain of Rho GDP-dissociation inhibitor directs N-terminal inhibitory peptide to GTPases.
Authors: Gosser, Y.Q. / Nomanbhoy, T.K. / Aghazadeh, B. / Manor, D. / Combs, C. / Cerione, R.A. / Rosen, M.K.
History
DepositionMar 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: transforming protein rhoA
E: rho GDP dissociation inhibitor alpha
C: transforming protein rhoA
F: rho GDP dissociation inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2928
Polymers89,3574
Non-polymers9354
Water00
1
A: transforming protein rhoA
E: rho GDP dissociation inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1464
Polymers44,6792
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: transforming protein rhoA
F: rho GDP dissociation inhibitor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1464
Polymers44,6792
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-31 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.300, 139.300, 253.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99947, -0.02832, -0.01623), (0.02808, -0.9995, 0.01482), (-0.01664, 0.01436, 0.99976)
Vector: 66.16257, 122.12522, -0.37127)

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Components

#1: Protein transforming protein rhoA / GTP-binding protein rhoA / GTPASE RHOA


Mass: 21440.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: COEXPRESSION WITH RHOGDI; / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): SY1 / References: UniProt: P61586
#2: Protein rho GDP dissociation inhibitor alpha / rho GDI 1


Mass: 23238.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: COEXPRESSION WITH RHOA / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): SY1 / References: UniProt: P52565
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 3.6 Å3/Da / Density % sol: 66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: CRYSTALS GROWN BY VAPOR DIFFUSION IN A SITTING DROP USING EQUAL VOLUMES OF PROTEIN AND RESERVOIR. CRYSTALLIZATION OCCURED OVER A PERIOD OF SEVERAL DAYS AT 20 DEGREE CELSIUS. PROTEIN (15 ...Details: CRYSTALS GROWN BY VAPOR DIFFUSION IN A SITTING DROP USING EQUAL VOLUMES OF PROTEIN AND RESERVOIR. CRYSTALLIZATION OCCURED OVER A PERIOD OF SEVERAL DAYS AT 20 DEGREE CELSIUS. PROTEIN (15 MG/ML) WAS IN 25MM TRIS-HCL, PH=8.0, 100MM NACL, 5MM MGCL2. RESERVOIR CONTAINED: 51% SATURATED AMMONIUM SULFATE, 100 MM SODIUM ACETATE, PH=5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 8.2
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
225 mMTris-HCl1drop
3100 mM1dropNaCl
45 mM1dropMgCl2
551 %satammonium sulfate1reservoir
6100 mM1reservoirCH3COONa

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8373 Å / Relative weight: 1
ReflectionResolution: 4→40 Å / Num. obs: 12817 / % possible obs: 99.1 % / Redundancy: 10.2 % / Rsym value: 0.061 / Net I/σ(I): 12.1
Reflection shellResolution: 4→4.09 Å / Rsym value: 0.193 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 130318 / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.193

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Processing

Software
NameClassification
CCP4model building
MLPHAREphasing
AMoREphasing
Omodel building
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MAD / Highest resolution: 5 Å
Details: MODEL NOT REFINED DUE TO EXTREME ANISOTROPY THE ELECTRON DENSITY MAP FOR THIS STRUCTURE WAS PHASED TO 5 ANGSTROMS USING MAD AND MIR PHASING TECHNIQUES. THE HIGH RESOLUTION STRUCTURES OF RHOA ...Details: MODEL NOT REFINED DUE TO EXTREME ANISOTROPY THE ELECTRON DENSITY MAP FOR THIS STRUCTURE WAS PHASED TO 5 ANGSTROMS USING MAD AND MIR PHASING TECHNIQUES. THE HIGH RESOLUTION STRUCTURES OF RHOA (1FTN) AND RHOGDI (1RHO) WERE FIT INTO THE 5A ELECTRON DENSITY MAP. RESIDUAL DENSITY WAS OBSERVED IN THE MAP THAT CONSTITUTE STRUCTURAL FEATURES FOR C-TERMINAL RESIDUES OF RHOA AND N-TERMINAL RESIDUES FOR RHOGDI. C-ALPHA ATOMS ARE MODELED FOR THESE RESIDUES TO PROVIDE A QUALITATIVE DESCRIPTION OF THE TERTIARY STRUCTURE OBSERVED AT 5A RESOLUTION
Refinement stepCycle: LAST / Highest resolution: 5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5120 0 58 0 5178

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