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- PDB-7dn9: Crystal structure of Salmonella effector in complex with NAD and ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dn9 | ||||||
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Title | Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1 | ||||||
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![]() | TRANSFERASE / ADP-ribosyltransferase | ||||||
Function / homology | ![]() mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / Nef Mediated CD4 Down-regulation / dendritic spine organization / long-term synaptic depression ...mitotic cleavage furrow ingression / trans-Golgi Network Vesicle Budding / Glycosphingolipid transport / regulation of receptor internalization / regulation of Arp2/3 complex-mediated actin nucleation / Intra-Golgi traffic / Synthesis of PIPs at the Golgi membrane / 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 / 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 / sarcomere / small monomeric GTPase / intracellular protein transport / cellular response to virus / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / focal adhesion / GTPase activity / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ding, J. / Shao, F. | ||||||
![]() | ![]() Title: ARF GTPases activate Salmonella effector SopF to ADP-ribosylate host V-ATPase and inhibit endomembrane damage-induced autophagy. Authors: Xu, Y. / Cheng, S. / Zeng, H. / Zhou, P. / Ma, Y. / Li, L. / Liu, X. / Shao, F. / Ding, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 376.2 KB | Display | ![]() |
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PDB format | ![]() | 306.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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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: 35443.977 Da / Num. of mol.: 4 / Mutation: E325D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: STM1239 / Plasmid: pGEX6p-2 / Production host: ![]() ![]() #2: Protein | Mass: 18936.600 Da / Num. of mol.: 4 / Mutation: Q71L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-NAD / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GDP / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 13% PEG 3350, 300mM sodium citrate, 100mM Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.287→46.92 Å / Num. obs: 33860 / % possible obs: 97.1 % / Redundancy: 2.86 % / CC1/2: 0.975 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.193 / Net I/σ(I): 5.79 |
Reflection shell | Resolution: 3.29→3.37 Å / Redundancy: 2.63 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.03 / Num. unique obs: 2301 / CC1/2: 0.733 / Rrim(I) all: 0.625 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.29→46.91 Å
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Refine LS restraints |
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LS refinement shell |
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