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Yorodumi- PDB-6j7f: Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j7f | ||||||||||||
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Title | Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP | ||||||||||||
Components |
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Keywords | LIPID BINDING PROTEIN / lipid transferase | ||||||||||||
Function / homology | Function and homology information protein prenyltransferase activity / protein geranylgeranyltransferase type II / protein-cysteine S-palmitoyltransferase activity / Rab-protein geranylgeranyltransferase complex / vesicle targeting / basal dendrite / Intra-Golgi traffic / Rab geranylgeranyltransferase activity / protein geranylgeranylation / SNARE complex ...protein prenyltransferase activity / protein geranylgeranyltransferase type II / protein-cysteine S-palmitoyltransferase activity / Rab-protein geranylgeranyltransferase complex / vesicle targeting / basal dendrite / Intra-Golgi traffic / Rab geranylgeranyltransferase activity / protein geranylgeranylation / SNARE complex / SNAP receptor activity / RAB geranylgeranylation / vesicle docking involved in exocytosis / apical dendrite / retrograde transport, endosome to Golgi / COPII-mediated vesicle transport / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / CDC42 GTPase cycle / RHOG GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / transport vesicle / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / RAC1 GTPase cycle / visual perception / endoplasmic reticulum-Golgi intermediate compartment membrane / protein modification process / cytoplasmic vesicle membrane / small GTPase binding / protein transport / endosome / cadherin binding / Golgi membrane / neuronal cell body / Golgi apparatus / endoplasmic reticulum / mitochondrion / zinc ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.883 Å | ||||||||||||
Authors | Goto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: To Be Published Title: Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP Authors: Goto-Ito, S. / Shirakawa, R. / Fukai, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j7f.cif.gz | 176.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j7f.ent.gz | 136.9 KB | Display | PDB format |
PDBx/mmJSON format | 6j7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/6j7f ftp://data.pdbj.org/pub/pdb/validation_reports/j7/6j7f | HTTPS FTP |
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-Related structure data
Related structure data | 6j7xC 6j6xS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
-Protein , 3 types, 3 molecules ABC
#1: Protein | Mass: 37986.520 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PTAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z6K3 |
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#2: Protein | Mass: 37371.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RABGGTB, GGTB / Production host: Escherichia coli (E. coli) References: UniProt: P53611, protein geranylgeranyltransferase type II |
#3: Protein | Mass: 22145.174 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: farnesyl-Ykt6 (C-terminal methylated) / Source: (gene. exp.) Homo sapiens (human) / Gene: YKT6 / Production host: Escherichia coli (E. coli) References: UniProt: O15498, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
-Non-polymers , 4 types, 4 molecules
#4: Chemical | ChemComp-TLA / |
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#5: Chemical | ChemComp-FAR / |
#6: Chemical | ChemComp-GER / |
#7: Chemical | ChemComp-DPO / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1M Ammonium Tartrate dibasic pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 35109 / % possible obs: 99.9 % / Redundancy: 16.2 % / Rsym value: 0.136 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.88→2.93 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1721 / Rsym value: 0.512 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J6X Resolution: 2.883→48.185 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.77
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.883→48.185 Å
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Refine LS restraints |
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LS refinement shell |
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