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Open data
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Basic information
Entry | Database: PDB / ID: 7bwt | ||||||
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Title | SopD-Rab8 complex structure | ||||||
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![]() | PROTEIN BINDING / complex | ||||||
Function / homology | ![]() neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / protein secretion by the type III secretion system / trans-Golgi network transport vesicle ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / protein secretion by the type III secretion system / trans-Golgi network transport vesicle / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / protein localization to cilium / non-motile cilium / vesicle docking involved in exocytosis / TBC/RABGAPs / ciliary membrane / host cell cytosol / ciliary base / Golgi organization / exocytosis / host cell membrane / : / protein secretion / cilium assembly / phagocytic vesicle / Anchoring of the basal body to the plasma membrane / centriole / protein tyrosine kinase binding / axonogenesis / small monomeric GTPase / ciliary basal body / trans-Golgi network membrane / regulation of autophagy / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / small GTPase binding / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / GTP binding / host cell plasma membrane / extracellular exosome / extracellular region / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jiang, K. / Tong, M. / Chen, Z. / Gao, X. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Salmonella effector protein SopD targets Rab8 to positively and negatively modulate the inflammatory response. Authors: Lian, H. / Jiang, K. / Tong, M. / Chen, Z. / Liu, X. / Galan, J.E. / Gao, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 252.3 KB | Display | ![]() |
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PDB format | ![]() | 169.2 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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Unit cell |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 38228.383 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) ![]() Gene: sopD, SBOV29801, AAK29_13240, AAP89_06495, ABO94_24435, AF480_02445, AF488_02240, AF489_05350, AIC76_09490, AU613_09175, AXR84_08085, AXU58_01945, C2253_22770, CD48_09420, CE87_05150, CET98_ ...Gene: sopD, SBOV29801, AAK29_13240, AAP89_06495, ABO94_24435, AF480_02445, AF488_02240, AF489_05350, AIC76_09490, AU613_09175, AXR84_08085, AXU58_01945, C2253_22770, CD48_09420, CE87_05150, CET98_05145, CQG18_13610, CVR97_12855, D4369_11200, D4380_01675, D4401_11680, D4E62_16310, D6360_15635, D7F20_20305, D7H43_13345, DJ388_17735, DKJ11_15155, DKU57_07540, DLM31_16580, DNV30_17025, DO698_06770, DOJ90_21490, DOQ88_13235, DPJ93_05695, DQ848_11540, DRM14_13800, DSF69_15975, DSR36_07735, DUW48_07630, EBO41_08190, EBP31_13605, EGU67_16485, EHB24_07065, EHC98_13260, EIW53_11070, GW08_01930, JO10_05155, LZ63_05365, NCTC13348_04477, NG18_06005, NU83_05435, QA89_11160, QB40_04780, QD15_03440, RJ78_02245, SAMEA4398682_00981, Y934_05005, YG50_06290, YI33_24045, YR17_16440, ZB89_12730, ZC54_04780 Production host: ![]() ![]() |
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#2: Protein | Mass: 20875.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 133 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-GDP / | #6: Chemical | ChemComp-MG / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.22 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.05M Sodium cacodylate trihydrate pH 6.5, 0.2 M MgCl2, 11.5% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 18, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→57.33 Å / Num. obs: 36383 / % possible obs: 99 % / Redundancy: 9 % / Biso Wilson estimate: 68.22 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Net I/σ(I): 19.32 |
Reflection shell | Resolution: 2.3→2.38 Å / Num. unique obs: 5694 / CC1/2: 0.566 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CPC,4LHW Resolution: 2.3→57.33 Å / SU ML: 0.3308 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3886
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 85.47 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→57.33 Å
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Refine LS restraints |
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LS refinement shell |
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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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