+Open data
-Basic information
Entry | Database: PDB / ID: 1upt | ||||||
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Title | Structure of a complex of the golgin-245 GRIP domain with Arl1 | ||||||
Components |
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Keywords | HYDROLASE/PROTEIN-BINDING / COMPLEX (GTPASE-GOLGIN) / GOLGIN-245 / GRIP / ARL1 / GOLGIN / GTPASE / G-PROTEIN / GOLGI / GRIP DIMER / PROTEIN SORTING / VESICLE TRAFFICKING / HYDROLASE-PROTEIN-BINDING complex | ||||||
Function / homology | Function and homology information phospholipase D activator activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / Golgi organization / enzyme activator activity ...phospholipase D activator activity / toxin metabolic process / Retrograde transport at the Trans-Golgi-Network / Golgi vesicle transport / Signaling by membrane-tethered fusions of PDGFRA or PDGFRB / protein localization to Golgi apparatus / Golgi to plasma membrane protein transport / retrograde transport, endosome to Golgi / Golgi organization / enzyme activator activity / positive regulation of axon extension / vesicle-mediated transport / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / small GTPase binding / GTPase binding / protein domain specific binding / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1.7 Å | ||||||
Authors | Panic, B. / Perisic, O. / Veprintsev, D.B. / Williams, R.L. / Munro, S. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: Structural Basis for Arl1-Dependent Targeting of Homodimeric Grip Domains to the Golgi Apparatus Authors: Panic, B. / Perisic, O. / Veprintsev, D.B. / Williams, R.L. / Munro, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1upt.cif.gz | 193.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1upt.ent.gz | 163.7 KB | Display | PDB format |
PDBx/mmJSON format | 1upt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/1upt ftp://data.pdbj.org/pub/pdb/validation_reports/up/1upt | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE GRIP DOMAIN FOMES A DIMER IN SOLUTION . THERE ARE TWOGRIP DOMAIN DIMERS IN THE ASYMMETRIC UNIT. THESE DIMERS ARECHAINS B/D AND CHAINS F/H. SINCE EACH OF THESE DIMERS ISIN COMPLEX WITH ARL1, THE ENTRY IS GIVEN AS TETRAMERIC. |
-Components
#1: Protein | Mass: 19699.580 Da / Num. of mol.: 4 / Fragment: RESIDUES 15-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPCG / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P40616 #2: Protein | Mass: 7407.808 Da / Num. of mol.: 4 / Fragment: GRIP DOMAIN RESIDUES 2170-2228 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPCG / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13439 #3: Chemical | ChemComp-GTP / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Compound details | MOL_ID 1 MAY PLAY A ROLE IN VESICULAR TRANSPORT FROM THE TRANS- GOLGI. MOL_ID 2 BELONGS TO THE ...MOL_ID 1 MAY PLAY A ROLE IN VESICULAR TRANSPORT FROM THE TRANS- GOLGI. MOL_ID 2 BELONGS TO THE SMALL GTPASE SUPERFAMIL | Sequence details | THE SEQUENCE OF CHAINS B, D, F AND H ARE ANNOTATED AS A SPLICE ISOFORM OF GOA4_HUMAN, WHICH HAS A ...THE SEQUENCE OF CHAINS B, D, F AND H ARE ANNOTATED AS A SPLICE ISOFORM OF GOA4_HUMAN, WHICH HAS A MODIFIED AT THE C-TERMINUS (FTSPRSGIF -> SWLRSSS). THE ID OF THIS VARIABLE ISOFORM IS ANNOTATED AS VSP_004275 IN THE SWISS-PROT ENTRY FOR THIS PROTEIN. 12OCT,2003. | |
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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: 2.1 Å3/Da / Density % sol: 40 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: GROWTH IN 20% PEG 3350, 0.2M TRIS-HCL PH 8.5. RESERVOIR EXCHANGED FOR 31% PEG 3350, 31% PEG 3350, 0.2M TRIS-HCL PH 8.5, FROZEN IN 31% PEG 3350, 0.2M TRIS-HCL PH 8.5. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7.5 / 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: ESRF / Beamline: ID14-4 / Wavelength: 0.97925,0.97942,0.93928 | ||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 2003 / Details: TORROIDAL MIRROR | ||||||||||||
Radiation | Monochromator: SI111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→67 Å / Num. obs: 94192 / % possible obs: 98.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.9 | ||||||||||||
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1 / % possible all: 92.3 | ||||||||||||
Reflection | *PLUS Highest resolution: 1.7 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.062 | ||||||||||||
Reflection shell | *PLUS % possible obs: 92.3 % |
-Processing
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Refinement | Method to determine structure: DIRECT METHODS / Resolution: 1.7→67.42 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.388 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.126 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.97 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→67.42 Å
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