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Yorodumi- PDB-1kzo: PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYLATED K-RAS4B P... -
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-Basic information
Entry | Database: PDB / ID: 1kzo | ||||||
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Title | PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH FARNESYLATED K-RAS4B PEPTIDE PRODUCT AND FARNESYL DIPHOSPHATE SUBSTRATE BOUND SIMULTANEOUSLY | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE SUBSTRATE / FTASE / PFT / PFTASE / FT / FPT / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / FARNESYL PROTEIN TRANSFERASE / CAAX / RAS / CANCER / PRODUCT / SUBSTRATE / TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX | ||||||
Function / homology | Function and homology information Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase ...Apoptotic cleavage of cellular proteins / Inactivation, recovery and regulation of the phototransduction cascade / RAS processing / protein geranylgeranyltransferase activity / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesylation / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / regulation of fibroblast proliferation / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / farnesyltranstransferase activity / forebrain astrocyte development / microtubule associated complex / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / enzyme-linked receptor protein signaling pathway / Rac protein signal transduction / positive regulation of nitric-oxide synthase biosynthetic process / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / alpha-tubulin binding / SHC1 events in ERBB4 signaling / : / Signalling to RAS / SHC-related events triggered by IGF1R / glial cell proliferation / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / positive regulation of cell cycle / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / positive regulation of glial cell proliferation / homeostasis of number of cells within a tissue / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / response to cytokine / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / regulation of long-term neuronal synaptic plasticity / wound healing / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
Citation | Journal: Nature / Year: 2002 Title: The Reaction Path of Protein Farnesyltransferase at Atomic Resolution Authors: Long, S.B. / Casey, P.J. / Beese, L.S. #1: Journal: Structure / Year: 2000 Title: The Basis for K-Ras4B Binding Specificity to Protein Farnesyltransferase Revealed by 2A Resolution Ternary Complex Structures Authors: Long, S.B. / Casey, P.J. / Beese, L.S. #2: Journal: Science / Year: 1997 Title: Crystal Structure of Protein Farnesyltransferase at 2.25A Resolution Authors: Park, H.W. / Boduluri, S.R. / Moomaw, J.F. / Casey, P.J. / Beese, L.S. #3: Journal: Biochemistry / Year: 1998 Title: Co-Crystal Structure of Mammalian Protein Farnesyltransferase with a Farnesyl Diphosphate Substrate Authors: Long, S.B. / Casey, P.J. / Beese, L.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kzo.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kzo.ent.gz | 134.2 KB | Display | PDB format |
PDBx/mmJSON format | 1kzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1kzo_validation.pdf.gz | 685.8 KB | Display | wwPDB validaton report |
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Full document | 1kzo_full_validation.pdf.gz | 692.5 KB | Display | |
Data in XML | 1kzo_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 1kzo_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/1kzo ftp://data.pdbj.org/pub/pdb/validation_reports/kz/1kzo | HTTPS FTP |
-Related structure data
Related structure data | 1kzpC 1d8dS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit of protein farnesyltransferase (FTase) is a heterodimer of alpha and beta subunits. There is one FTase heterodimer per asymmetric unit. |
-Components
-Protein Farnesyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 44098.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04631, squalene synthase |
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#2: Protein | Mass: 48722.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02293, squalene synthase |
-Protein/peptide , 1 types, 1 molecules C
#3: Protein/peptide | Mass: 1298.723 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS. References: UniProt: P01118, UniProt: P01116*PLUS |
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-Non-polymers , 5 types, 432 molecules
#4: Chemical | ChemComp-ZN / |
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#5: Chemical | ChemComp-FPP / |
#6: Chemical | ChemComp-ACY / |
#7: Chemical | ChemComp-FAR / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.57 % | ||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG 8000, Ammonium Acetate, Magnesium Chloride, DTT, Tris-HCl, pH 5.70, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 5.7 / Details: Long, S.B., (2000) Structure, 8, 209. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 7, 2000 / Details: Mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 56209 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 4.51 % / Biso Wilson estimate: 32.8 Å2 / Rsym value: 0.089 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 2.2→2.23 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1705 / Rsym value: 0.63 / % possible all: 87.9 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. measured all: 253335 / Rmerge(I) obs: 0.089 |
Reflection shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rmerge(I) obs: 0.56 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1D8D Resolution: 2.2→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor all: 0.162 / Rfactor obs: 0.159 / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.16 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.255 |