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- PDB-1n4s: Protein Geranylgeranyltransferase type-I Complexed with GGPP and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1n4s | ||||||
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Title | Protein Geranylgeranyltransferase type-I Complexed with GGPP and a Geranylgeranylated KKKSKTKCVIL Peptide Product | ||||||
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![]() | TRANSFERASE / protein geranylgeranyltransferase type-I / GGTase / geranylgeranyl / protein prenylation / CaaX / lipid modification / rap2b | ||||||
Function / homology | ![]() 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 / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / negative regulation of nitric-oxide synthase biosynthetic process / forebrain astrocyte development / microtubule associated complex / negative regulation of epithelial cell differentiation / regulation of synaptic transmission, GABAergic / type I pneumocyte differentiation / epithelial tube branching involved in lung morphogenesis / heterocyclic compound binding / 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 / SHC1 events in ERBB4 signaling / alpha-tubulin binding / : / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / glial cell proliferation / 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 / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of cell cycle / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / 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 / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / 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 / Constitutive Signaling by EGFRvIII / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / response to organic cyclic compound Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Taylor, J.S. / Reid, T.S. / Casey, P.J. / Beese, L.S. | ||||||
![]() | ![]() Title: Structure of mammalian protein geranylgeranyltransferase type-I Authors: Taylor, J.S. / Reid, T.S. / Terry, K.L. / Casey, P.J. / Beese, L.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 818.4 KB | Display | ![]() |
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PDB format | ![]() | 694.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 12 molecules ACEGIKBDFHJL
#1: Protein | Mass: 44098.145 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q04631, protein farnesyltransferase, protein geranylgeranyltransferase type I #2: Protein | Mass: 42466.176 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P53610, protein geranylgeranyltransferase type I |
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-Protein/peptide , 1 types, 6 molecules MNOPQR
#3: Protein/peptide | Mass: 1280.685 Da / Num. of mol.: 6 / Source method: obtained synthetically Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE GERANYLGERANYL LIPID WAS ADDED BY THE ENZYME. Source: (synth.) ![]() |
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-Non-polymers , 5 types, 1323 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GRG.gif)
![](data/chem/img/GER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GRG.gif)
![](data/chem/img/GER.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-GRG / #7: Chemical | ChemComp-GER / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.77 Å3/Da / Density % sol: 74.21 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: ammonium sulfate, sodium citrate, dithiothreitol , pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2002 / Details: Pt-coated toroidal Si mirror |
Radiation | Monochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→29.98 Å / Num. all: 300000 / Num. obs: 300000 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 56.3 Å2 / Rsym value: 0.069 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.43 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. measured all: 1011902 / Rmerge(I) obs: 0.069 |
Reflection shell | *PLUS Highest resolution: 2.6 Å / % possible obs: 100 % / Rmerge(I) obs: 0.435 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.7338 Å2 / ksol: 0.358207 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.315 / Rfactor Rwork: 0.293 |