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Yorodumi- PDB-7opp: Crystal structure of the Rab27a fusion with Slp2a-RBDa1 effector ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7opp | ||||||
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Title | Crystal structure of the Rab27a fusion with Slp2a-RBDa1 effector for SF4 pocket drug targeting | ||||||
Components | Synaptotagmin-like protein 2,Ras-related protein Rab-27A | ||||||
Keywords | EXOCYTOSIS / Rab27 / GTPase / Slp2a / exosome | ||||||
Function / homology | Function and homology information multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / melanosome localization / natural killer cell degranulation / exosomal secretion / melanosome transport / Weibel-Palade body / neurexin family protein binding ...multivesicular body organization / cytotoxic T cell degranulation / positive regulation of constitutive secretory pathway / positive regulation of regulated secretory pathway / melanosome localization / natural killer cell degranulation / exosomal secretion / melanosome transport / Weibel-Palade body / neurexin family protein binding / exocytic vesicle / melanocyte differentiation / melanosome membrane / multivesicular body sorting pathway / RAB geranylgeranylation / myosin V binding / multivesicular body membrane / RAB GEFs exchange GTP for GDP on RABs / Regulation of MITF-M-dependent genes involved in pigmentation / complement-dependent cytotoxicity / vesicle docking involved in exocytosis / positive regulation of reactive oxygen species biosynthetic process / synaptic vesicle transport / Insulin processing / phosphatidylserine binding / exocytosis / positive regulation of exocytosis / antigen processing and presentation / protein secretion / photoreceptor outer segment / phosphatase binding / positive regulation of phagocytosis / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / small monomeric GTPase / G protein activity / secretory granule / intracellular protein transport / small GTPase binding / specific granule lumen / GDP binding / blood coagulation / melanosome / late endosome / lysosome / apical plasma membrane / protein domain specific binding / GTPase activity / dendrite / Neutrophil degranulation / positive regulation of gene expression / GTP binding / Golgi apparatus / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å | ||||||
Authors | Jamshidiha, M. / Tersa, M. / Lanyon-Hogg, T. / Perez-Dorado, I. / Sutherell, C.L. / De Vita, E. / Morgan, R.M.L. / Tate, E.W. / Cota, E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Rsc Med Chem / Year: 2022 Title: Identification of the first structurally validated covalent ligands of the small GTPase RAB27A. Authors: Jamshidiha, M. / Lanyon-Hogg, T. / Sutherell, C.L. / Craven, G.B. / Tersa, M. / De Vita, E. / Brustur, D. / Perez-Dorado, I. / Hassan, S. / Petracca, R. / Morgan, R.M. / Sanz-Hernandez, M. / ...Authors: Jamshidiha, M. / Lanyon-Hogg, T. / Sutherell, C.L. / Craven, G.B. / Tersa, M. / De Vita, E. / Brustur, D. / Perez-Dorado, I. / Hassan, S. / Petracca, R. / Morgan, R.M. / Sanz-Hernandez, M. / Norman, J.C. / Armstrong, A. / Mann, D.J. / Cota, E. / Tate, E.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7opp.cif.gz | 134.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7opp.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 7opp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7opp_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7opp_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7opp_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | 7opp_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/op/7opp ftp://data.pdbj.org/pub/pdb/validation_reports/op/7opp | HTTPS FTP |
-Related structure data
Related structure data | 7opqC 7oprC 3bc1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 25956.184 Da / Num. of mol.: 2 / Mutation: Q78L,C123S,C188S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SYTL2, KIAA1597, SGA72M, SLP2, SLP2A, RAB27A, RAB27 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q9HCH5, UniProt: P51159, small monomeric GTPase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.47 Å3/Da / Density % sol: 72.51 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.5 M Sodium phosphate monobasic monohydrate, 0.1 M Sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 24, 2016 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.32→58.85 Å / Num. obs: 40486 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 36.64 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02731 / Rpim(I) all: 0.02731 / Rrim(I) all: 0.03862 / Net I/σ(I): 20.04 |
Reflection shell | Resolution: 2.32→2.403 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2401 / Mean I/σ(I) obs: 3.29 / Num. unique obs: 3976 / CC1/2: 0.844 / CC star: 0.957 / Rpim(I) all: 0.2401 / Rrim(I) all: 0.3395 / % possible all: 99.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BC1 Resolution: 2.32→58.85 Å / SU ML: 0.227 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.4598 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.05 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.32→58.85 Å
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Refine LS restraints |
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LS refinement shell |
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