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Yorodumi- PDB-1n4q: Protein Geranylgeranyltransferase type-I Complexed with a GGPP An... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n4q | ||||||
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Title | Protein Geranylgeranyltransferase type-I Complexed with a GGPP Analog and a KKKSKTKCVIL Peptide | ||||||
Components |
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Keywords | TRANSFERASE / protein geranylgeranyltransferase type-I / GGTase / geranylgeranyl / protein prenylation / CaaX / lipid modification / rap2b | ||||||
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 / 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 / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / 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 / 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 / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / 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 / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / visual learning / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / response to organic cyclic compound Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Taylor, J.S. / Reid, T.S. / Casey, P.J. / Beese, L.S. | ||||||
Citation | Journal: EMBO J. / Year: 2003 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n4q.cif.gz | 808.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n4q.ent.gz | 685.3 KB | Display | PDB format |
PDBx/mmJSON format | 1n4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n4q_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 1n4q_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1n4q_validation.xml.gz | 151.4 KB | Display | |
Data in CIF | 1n4q_validation.cif.gz | 206.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/1n4q ftp://data.pdbj.org/pub/pdb/validation_reports/n4/1n4q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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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
-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.) Rattus norvegicus (Norway rat) / Gene: Fnta / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm) 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.) Rattus norvegicus (Norway rat) / Gene: Pggt1b / Plasmid: ATCC 63134 / Production host: Spodoptera frugiperda (fall armyworm) 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.) Homo sapiens (human) / References: UniProt: P01116*PLUS |
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-Non-polymers , 5 types, 1137 molecules
#4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-MGM / #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-GER / | #8: Water | ChemComp-HOH / | |
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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: 4.75 Å3/Da / Density % sol: 74.13 % | ||||||||||||||||||||||||||||||||||||||||||
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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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2001 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→33.12 Å / Num. all: 356309 / Num. obs: 356309 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 45.8 Å2 / Rsym value: 0.056 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.35 / % possible all: 87.1 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 355317 / % possible obs: 93 % / Num. measured all: 997257 / Rmerge(I) obs: 0.056 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 87.1 % / Rmerge(I) obs: 0.352 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.99 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber Details: GGTase-I initially solved at 2.7 A resolution in an I222 space group using SIRAS. This model was then used for molecular replacement in the C2 space group. NCS restraints employed during ...Details: GGTase-I initially solved at 2.7 A resolution in an I222 space group using SIRAS. This model was then used for molecular replacement in the C2 space group. NCS restraints employed during refinement of the c2 structure.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.2596 Å2 / ksol: 0.373144 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→29.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.007 / 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: 0.356 / Rfactor Rwork: 0.334 |