+Open data
-Basic information
Entry | Database: PDB / ID: 4c0a | ||||||
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Title | Arf1(Delta1-17)in complex with BRAG2 Sec7-PH domain | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / ENDOCYTOSIS | ||||||
Function / homology | Function and homology information Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Synthesis of PIPs at the plasma membrane / Golgi Associated Vesicle Biogenesis / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Lysosome Vesicle Biogenesis / regulation of ARF protein signal transduction / regulation of receptor internalization ...Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Synthesis of PIPs at the plasma membrane / Golgi Associated Vesicle Biogenesis / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / Lysosome Vesicle Biogenesis / regulation of ARF protein signal transduction / regulation of receptor internalization / MHC class II antigen presentation / regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of keratinocyte migration / dendritic spine development / positive regulation of focal adhesion disassembly / dendritic spine organization / long-term synaptic depression / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / small monomeric GTPase / intracellular protein transport / synaptic vesicle / actin cytoskeleton organization / postsynaptic density / neuron projection / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / lipid binding / GTP binding / nucleolus / Golgi apparatus / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) BOS TAURUS (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | ||||||
Authors | Aizel, K. / Biou, V. / Navaza, J. / Duarte, L. / Campanacci, V. / Cherfils, J. / Zeghouf, M. | ||||||
Citation | Journal: PLoS Biol. / Year: 2013 Title: Integrated conformational and lipid-sensing regulation of endosomal ArfGEF BRAG2. Authors: Aizel, K. / Biou, V. / Navaza, J. / Duarte, L.V. / Campanacci, V. / Cherfils, J. / Zeghouf, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c0a.cif.gz | 859.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c0a.ent.gz | 713.7 KB | Display | PDB format |
PDBx/mmJSON format | 4c0a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/4c0a ftp://data.pdbj.org/pub/pdb/validation_reports/c0/4c0a | 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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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 44409.500 Da / Num. of mol.: 4 / Fragment: SEC7 AND PH DOMAIN, RESIDUES 390-763 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLD / References: UniProt: Q6DN90 #2: Protein | Mass: 18822.455 Da / Num. of mol.: 4 / Fragment: DELTA17 ARF1, RESIDUES 18-181 Source method: isolated from a genetically manipulated source Details: GDP-3P LIGAND / Source: (gene. exp.) BOS TAURUS (cattle) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: P84080 #3: Chemical | ChemComp-G3D / Sequence details | ARF1 WAS DELETED FROM ITS 17 FIRST AMINO ACIDS IN THE STRUCTURE ISOFORM 2 AND IN THE STRUCTURE ...ARF1 WAS DELETED FROM ITS 17 FIRST AMINO ACIDS IN THE STRUCTURE ISOFORM 2 AND IN THE STRUCTURE SEQUENCE REMAINS A PART OF THE CLEAVED 6-HISTAG GAMGSGIP | |
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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: 2.32 Å3/Da / Density % sol: 46.99 % / Description: NONE |
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Crystal grow | pH: 6 Details: 0.15 M AMMONIUM SULFATE, 0.1 M MES PH 6 AND 16% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 10, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Monochromator: CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→42.8 Å / Num. obs: 67437 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Biso Wilson estimate: 61.36 Å2 / Rmerge(I) obs: 0.03 / Rsym value: 0.201 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 3.3→3.4 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 1.94 / Rsym value: 0.735 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1R8S AND 3QWM Resolution: 3.3→42.84 Å / Cor.coef. Fo:Fc: 0.9122 / Cor.coef. Fo:Fc free: 0.867 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.549 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
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Displacement parameters | Biso mean: 69.56 Å2
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Refine analyze | Luzzati coordinate error obs: 0.715 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→42.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.4 Å / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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