+Open data
-Basic information
Entry | Database: PDB / ID: 3o47 | ||||||
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Title | Crystal structure of ARFGAP1-ARF1 fusion protein | ||||||
Components | ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1 | ||||||
Keywords | HYDROLASE / HYDROLASE ACTIVATOR / structural genomics consortium / GTPase activation / fusion protein / chimera protein / SGC | ||||||
Function / homology | Function and homology information mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of ARF protein signal transduction / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / XBP1(S) activates chaperone genes / Nef Mediated CD4 Down-regulation / dendritic spine organization ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / regulation of ARF protein signal transduction / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / XBP1(S) activates chaperone genes / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression / COPI-dependent Golgi-to-ER retrograde traffic / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / cell leading edge / Synthesis of PIPs at the plasma membrane / regulation of endocytosis / intracellular copper ion homeostasis / COPI-mediated anterograde transport / vesicle-mediated transport / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / GTPase activator activity / sarcomere / small monomeric GTPase / intracellular protein transport / cellular response to virus / protein transport / Clathrin-mediated endocytosis / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / synapse / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Wang, H. / Tong, Y. / Nedyalkova, L. / Tempel, W. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. ...Wang, H. / Tong, Y. / Nedyalkova, L. / Tempel, W. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: to be published Title: Crystal structure of ARFGAP1-ARF1 fusion protein Authors: Wang, H. / Tong, Y. / Nedyalkova, L. / Tempel, W. / Guan, X. / Crombet, L. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3o47.cif.gz | 128.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3o47.ent.gz | 97.1 KB | Display | PDB format |
PDBx/mmJSON format | 3o47.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o4/3o47 ftp://data.pdbj.org/pub/pdb/validation_reports/o4/3o47 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37945.070 Da / Num. of mol.: 2 Fragment: ARF1GAP, UNP residues 1-140, ARF1, UNP residues 11-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGAP1, ARF1GAP, ARF1 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-V2R-pRARE2 / References: UniProt: Q8N6T3, UniProt: P84077 #2: Chemical | #3: Chemical | |
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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: 2.66 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 20% PEG-3350, 0.2M trilithium sulfate, pH not applicable, vapor diffusion, temperature 291K PH range: not applicable |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 11, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→40 Å / Num. obs: 20250 / % possible obs: 99.9 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.116 / Χ2: 1.627 / Net I/σ(I): 8.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entries 1HUR, 3DWD Resolution: 2.8→39.65 Å / Cor.coef. Fo:Fc: 0.9166 / Cor.coef. Fo:Fc free: 0.8932 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 Details: Programs COOT and PHENIX and the MOLPROBITY server were also used during refinement.
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Displacement parameters | Biso max: 132.76 Å2 / Biso mean: 65.1668 Å2 / Biso min: 34.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.387 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.95 Å / Total num. of bins used: 10
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