|Entry||Database: PDB / ID: 1d8d|
|Title||CO-CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A K-RAS4B PEPTIDE SUBSTRATE AND FPP ANALOG AT 2.0A RESOLUTION|
|Keywords||TRANSFERASE / FTASE / PFT / PFTASE / FARNESYLTRANSFERASE / FARNESYL TRANSFERASE / CAAX / RAS / CANCER|
|Function / homology|
Function and homology information
Inactivation, recovery and regulation of the phototransduction cascade / Apoptotic cleavage of cellular proteins / RAS processing / positive regulation of tubulin deacetylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase complex / protein farnesyltransferase ...Inactivation, recovery and regulation of the phototransduction cascade / Apoptotic cleavage of cellular proteins / RAS processing / positive regulation of tubulin deacetylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / protein farnesyltransferase complex / protein farnesyltransferase / protein farnesyltransferase activity / neurotransmitter receptor metabolic process / regulation of fibroblast proliferation / acetylcholine receptor regulator activity / protein farnesylation / Rab geranylgeranyltransferase activity / response to inorganic substance / positive regulation of deacetylase activity / protein geranylgeranylation / protein prenylation / farnesyltranstransferase activity / negative regulation of nitric-oxide synthase biosynthetic process / endocrine signaling / forebrain astrocyte development / GMP binding / microtubule associated complex / LRR domain binding / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / response to mineralocorticoid / positive regulation of Rac protein signal transduction / alpha-tubulin binding / RAS GTPase cycle mutants / Activation of RAS in B cells / positive regulation of nitric-oxide synthase biosynthetic process / RUNX3 regulates p14-ARF / RAS signaling downstream of NF1 loss-of-function variants / response to isolation stress / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / homeostasis of number of cells within a tissue / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by FGFR3 fusions in cancer / Estrogen-stimulated signaling through PRKCZ / Signaling by PDGFRA extracellular domain mutants / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / negative regulation of cell differentiation / positive regulation of cell cycle / Signaling by FLT3 ITD and TKD mutants / Erythropoietin activates RAS / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Tie2 Signaling / Signaling by CSF3 (G-CSF) / Signaling by FGFR3 point mutants in cancer / G protein activity / FRS-mediated FGFR2 signaling / small monomeric GTPase / FRS-mediated FGFR4 signaling / Signaling by FGFR2 in disease / Ras activation upon Ca2+ influx through NMDA receptor / FRS-mediated FGFR1 signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / p38MAPK events / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / Downstream signal transduction / striated muscle cell differentiation / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / NCAM signaling for neurite out-growth / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / visual learning / VEGFR2 mediated cell proliferation / Ca2+ pathway / response to cytokine / response to glucocorticoid / regulation of long-term neuronal synaptic plasticity / RAF activation / Signaling by high-kinase activity BRAF mutants / FCERI mediated MAPK activation / positive regulation of fibroblast proliferation / Signaling by ERBB2 TMD/JMD mutants / MAP2K and MAPK activation
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / Protein prenyltransferase, alpha subunit / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Small GTPase, Ras-type ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / Protein prenyltransferase, alpha subunit / PFTB repeat / Prenyltransferase and squalene oxidase repeat / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Small GTPase, Ras-type / small GTPase Ras family profile. / Glycosyltransferase / Alpha/alpha barrel / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Small GTP-binding protein domain / Alpha Horseshoe / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Protein farnesyltransferase subunit beta / ACETATE ION / GTPase KRas / Chem-FII / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
Similarity search - Component
|Biological species||Rattus norvegicus (Norway rat)|
|Method||X-RAY DIFFRACTION / Resolution: 2 Å|
|Authors||Long, S.B. / Casey, P.J. / Beese, L.S.|
Journal: Structure Fold.Des. / Year: 2000
Title: The basis for K-Ras4B binding specificity to protein farnesyltransferase revealed by 2 A resolution ternary complex structures.
Authors: Long, S.B. / Casey, P.J. / Beese, L.S.
#1: 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.
|Structure viewer||Molecule: |
Downloads & links
A: farnesyltransferase (alpha subunit)
B: farnesyltransferase (beta subunit)
P: K-RAS4B PEPTIDE SUBSTRATE
-Farnesyltransferase ... , 2 types, 2 molecules A
|#1: Protein|| |
Mass: 44098.145 Da / Num. of mol.: 1 / Fragment: alpha subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04631, squalene synthase
|#2: Protein|| |
Mass: 48722.281 Da / Num. of mol.: 1 / Fragment: beta subunit
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q02293, squalene synthase
-Protein/peptide , 1 types, 1 molecules P
|#3: Protein/peptide|| |
Mass: 1298.723 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This synthetic peptide is derived from human K-Ras4B, residues 178-188.
References: UniProt: P01116
-Non-polymers , 4 types, 453 molecules
|#4: Chemical|| ChemComp-ZN / |
Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
Details: non-reactive FPP analog (FPT Inhibitor II, Calbiochem) Manne, V. et al. & Biller, S.A. (1995) Drug Dev. Res. 34,pg 121-137
|#6: Chemical|| ChemComp-FII / [(||#7: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3.1 Å3/Da / Density % sol: 60.35 %|
|Crystal grow||Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.7 |
Details: Peg 8000, ammonium acetate, DTT, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 290K
*PLUSTemperature: 17 ℃
|Components of the solutions|
|Diffraction||Mean temperature: 96 K|
|Diffraction source||Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418|
|Detector||Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 23, 1998|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.5418 Å / Relative weight: 1|
|Reflection||Resolution: 2→35 Å / Num. all: 77998 / Num. obs: 76088 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.9|
|Reflection shell||Resolution: 2→2.02 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.197 / Num. unique all: 2154 / % possible all: 83.9|
*PLUSNum. measured all: 320401
*PLUS% possible obs: 83.9 %
|Refinement||Resolution: 2→35 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Stereochemistry target values: Engh & Huber|
|Displacement parameters||Biso mean: 34.2 Å2|
|Refinement step||Cycle: LAST / Resolution: 2→35 Å|
|Refine LS restraints|
|LS refinement shell||Resolution: 2→2.09 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8 |
*PLUSName: X-PLOR / Version: 3.851 / Classification: refinement
|Refine LS restraints|
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