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Yorodumi- PDB-1r8q: FULL-LENGTH ARF1-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r8q | ||||||
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Title | FULL-LENGTH ARF1-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/EXCHANGE FACTOR / PROTEIN TRANSPORT-EXCHANGE FACTOR complex | ||||||
Function / homology | Function and homology information Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Glycosphingolipid transport / 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 / MHC class II antigen presentation ...Synthesis of PIPs at the Golgi membrane / trans-Golgi Network Vesicle Budding / Intra-Golgi traffic / Glycosphingolipid transport / 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 / MHC class II antigen presentation / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / inositol 1,4,5 trisphosphate binding / regulation of ARF protein signal transduction / dendritic spine organization / long-term synaptic depression / bicellular tight junction / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / small monomeric GTPase / adherens junction / intracellular protein transport / endocytosis / growth cone / actin cytoskeleton organization / postsynaptic density / neuron projection / Golgi membrane / GTPase activity / lipid binding / GTP binding / Golgi apparatus / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Renault, L. / Guibert, B. / Cherfils, J. | ||||||
Citation | Journal: Nature / Year: 2003 Title: Structural snapshots of the mechanism and inhibition of a guanine nucleotide exchange factor Authors: Renault, L. / Guibert, B. / Cherfils, J. | ||||||
History |
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Remark 600 | HETEROGEN For the hetero-atom with residue sequence number 601, a ZN ion was modelled to explain a ...HETEROGEN For the hetero-atom with residue sequence number 601, a ZN ion was modelled to explain a strong electron density corresponding to an ion (close to 2 GLU and 2 HIS residues) based only on the homology of the binding site with the ZN binding site in PDB 14FT. However, Zn was not present in the crystallization buffer. | ||||||
Remark 999 | SEQUENCE The engineered mutations in the Arno structure (F190Y, A191S, S198D, P208M) are Brefeldin ...SEQUENCE The engineered mutations in the Arno structure (F190Y, A191S, S198D, P208M) are Brefeldin A- sensitizing mutations. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r8q.cif.gz | 174.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r8q.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 1r8q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r8q_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1r8q_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1r8q_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 1r8q_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/1r8q ftp://data.pdbj.org/pub/pdb/validation_reports/r8/1r8q | HTTPS FTP |
-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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5 |
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6 |
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Unit cell |
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Details | The biological assembly is an hetero-dimer (chain A with E or chain B with F) |
-Components
-Protein , 2 types, 4 molecules ABEF
#1: Protein | Mass: 20721.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ARF1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P84080 #2: Protein | Mass: 23438.637 Da / Num. of mol.: 2 / Fragment: Sec7 domain (residues 50-252) / Mutation: F190Y/A191S/S198D/P208M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PSCD2, ARNO / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q99418 |
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-Non-polymers , 5 types, 352 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-ZN / | #7: 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: 2.54 Å3/Da / Density % sol: 51.56 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 19% Peg 3350, 175mM NH4 Fluoride, 100mM cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / 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: ID14-3 / Wavelength: 0.931 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→25 Å / Num. obs: 74905 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.77 % / Biso Wilson estimate: 27.28 Å2 / Rsym value: 0.087 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.86→1.88 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.424 / % possible all: 83.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→29.88 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.756 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 24.191 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.88 Å / Total num. of bins used: 47 /
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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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Refinement | *PLUS Lowest resolution: 25 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |