+Open data
-Basic information
Entry | Database: PDB / ID: 1cc0 | ||||||
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Title | CRYSTAL STRUCTURE OF THE RHOA.GDP-RHOGDI COMPLEX | ||||||
Components |
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Keywords | SIGNALING PROTEIN / RHO GTPASE / G-PROTEIN | ||||||
Function / homology | Function and homology information Rho GDP-dissociation inhibitor activity / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / 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 ...Rho GDP-dissociation inhibitor activity / aortic valve formation / alpha-beta T cell lineage commitment / mitotic cleavage furrow formation / bone trabecula morphogenesis / 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 / 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 synaptic vesicle cycle / 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 / regulation of systemic arterial blood pressure by endothelin / cerebral cortex cell migration / regulation of Rho protein signal transduction / negative regulation of cell migration involved in sprouting angiogenesis / cellular response to chemokine / beta selection / establishment of epithelial cell apical/basal polarity / negative regulation of cell size / regulation of modification of postsynaptic structure / RHO GTPases Activate ROCKs / negative regulation of oxidative phosphorylation / negative regulation of motor neuron apoptotic process / ERBB2 Regulates Cell Motility / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / PCP/CE pathway / RHO GTPases activate KTN1 / apolipoprotein A-I-mediated signaling pathway / positive regulation of podosome assembly / negative regulation of cell-substrate adhesion / positive regulation of alpha-beta T cell differentiation / ossification involved in bone maturation / odontogenesis / Wnt signaling pathway, planar cell polarity pathway / Sema4D mediated inhibition of cell attachment and migration / motor neuron apoptotic process / positive regulation of leukocyte adhesion to vascular endothelial cell / PI3K/AKT activation / wound healing, spreading of cells / apical junction complex / regulation of focal adhesion assembly / negative chemotaxis / myosin binding / EPHA-mediated growth cone collapse / stress fiber assembly / regulation of neuron projection development / RHOC GTPase cycle / positive regulation of cytokinesis / androgen receptor signaling pathway / cellular response to cytokine stimulus / cleavage furrow / CDC42 GTPase cycle / semaphorin-plexin signaling pathway / Rho protein signal transduction / RHOH GTPase cycle / ficolin-1-rich granule membrane / immunological synapse / RHOG GTPase cycle / mitotic spindle assembly / RHOA GTPase cycle / endothelial cell migration / RAC2 GTPase cycle / positive regulation of T cell migration / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / regulation of microtubule cytoskeleton organization / negative regulation of reactive oxygen species biosynthetic process / cytoplasmic microtubule organization / skeletal muscle tissue development / RHO GTPases activate PKNs / positive regulation of stress fiber assembly / GPVI-mediated activation cascade / EPHB-mediated forward signaling / RAC1 GTPase cycle / substantia nigra development / positive regulation of neuron differentiation / regulation of cell migration / substrate adhesion-dependent cell spreading / GTPase activator activity / cell-matrix adhesion / small monomeric GTPase / secretory granule membrane / G protein activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / cell periphery / RHO GTPases Activate Formins Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 5 Å | ||||||
Authors | Longenecker, 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 | Journal: Acta Crystallogr.,Sect.D / Year: 1999 Title: How RhoGDI binds Rho. Authors: Longenecker, K. / Read, P. / Derewenda, U. / Dauter, Z. / Liu, X. / Garrard, S. / Walker, L. / Somlyo, A.V. / Nakamoto, R.K. / Somlyo, A.P. / Derewenda, Z.S. #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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cc0.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cc0.ent.gz | 97 KB | Display | PDB format |
PDBx/mmJSON format | 1cc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1cc0_validation.pdf.gz | 930 KB | Display | wwPDB validaton report |
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Full document | 1cc0_full_validation.pdf.gz | 957.3 KB | Display | |
Data in XML | 1cc0_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 1cc0_validation.cif.gz | 26.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/1cc0 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/1cc0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99947, -0.02832, -0.01623), Vector: |
-Components
#1: Protein | 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 | 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 | #4: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 66 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8373 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1998 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8373 Å / Relative weight: 1 |
Reflection | Resolution: 4→40 Å / Num. obs: 12817 / % possible obs: 99.1 % / Redundancy: 10.2 % / Rsym value: 0.061 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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 step | Cycle: LAST / Highest resolution: 5 Å
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