+Open data
-Basic information
Entry | Database: PDB / ID: 2uzi | ||||||
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Title | Crystal structure of HRAS(G12V) - anti-RAS Fv complex | ||||||
Components |
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Keywords | SIGNALING PROTEIN/IMMUNE SYSTEM / SIGNAL TRANSDUCTION / IMMUNOGLOBULIN DOMAIN / MEMBRANE / ANTIBODY / ONCOGENE / PALMITATE / INTRABODY / DISEASE MUTATION / NUCLEOTIDE-BINDING / PROTO-ONCOGENE / CANCER THERAPY / GOLGI APPARATUS / PRENYLATION / METHYLATION / LIPOPROTEIN / GTP- BINDING / SIGNALING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Schwann cell development / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / protein-membrane adaptor activity / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / myelination / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / EPHB-mediated forward signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / positive regulation of MAP kinase activity / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / positive regulation of type II interferon production / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / positive regulation of fibroblast proliferation / cellular senescence / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tanaka, T. / williams, R.L. / Rabbitts, T.H. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Tumour Prevention by a Single Antibody Domain Targeting the Interaction of Signal Transduction Proteins with Ras. Authors: Tanaka, T. / Williams, R.L. / Rabbitts, T.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uzi.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uzi.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 2uzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/2uzi ftp://data.pdbj.org/pub/pdb/validation_reports/uz/2uzi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules R
#3: Protein | Mass: 18917.271 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRK172 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P01112 |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 12688.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRK-HISTEV-VH-RAS-VL / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 |
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#2: Antibody | Mass: 11220.517 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PRK-HISTEV-VH-RAS-VL / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 |
-Non-polymers , 4 types, 296 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-GTP / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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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: 2.15 Å3/Da / Density % sol: 38.2 % |
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Crystal grow | Details: PROTEIN WAS CRYSTALLIZED FROM 17-18 % PEG3350, 400 MM ZINC ACETATE, 100 MM SODIUM CACODYLATE, PH 5.8, 0.03 % DICHLOROMETHANE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 11, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→50.32 Å / Num. obs: 27214 / % possible obs: 98.2 % / Observed criterion σ(I): 3.7 / Redundancy: 3.38 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.42 |
Reflection shell | Resolution: 2→2.02 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.67 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AGP, 1A2Y Resolution: 2→41.89 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 4.749 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2→41.89 Å
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