+Open data
-Basic information
Entry | Database: PDB / ID: 4bx9 | ||||||
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Title | Human Vps33A in complex with a fragment of human Vps16 | ||||||
Components | (VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN ...) x 2 | ||||||
Keywords | PROTEIN TRANSPORT / HOPS / MEMBRANE TRAFFICKING / SEC1/MUNC18 PROTEINS / TETHERING | ||||||
Function / homology | Function and homology information regulation of developmental pigmentation / CORVET complex / HOPS complex / regulation of SNARE complex assembly / melanosome localization / endosomal vesicle fusion / vacuole fusion, non-autophagic / SARS-CoV-2 modulates autophagy / regulation of lysosomal lumen pH / lysosome localization ...regulation of developmental pigmentation / CORVET complex / HOPS complex / regulation of SNARE complex assembly / melanosome localization / endosomal vesicle fusion / vacuole fusion, non-autophagic / SARS-CoV-2 modulates autophagy / regulation of lysosomal lumen pH / lysosome localization / clathrin-coated vesicle / platelet formation / endosomal transport / endosome to lysosome transport / autophagosome maturation / vesicle-mediated transport / autophagosome / intracellular protein transport / recycling endosome / late endosome / late endosome membrane / actin binding / lysosome / early endosome / endosome membrane / endosome / lysosomal membrane / perinuclear region of cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Graham, S.C. / Wartosch, L. / Gray, S.R. / Scourfield, E.J. / Deane, J.E. / Luzio, J.P. / Owen, D.J. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2013 Title: Structural basis of Vps33A recruitment to the human HOPS complex by Vps16. Authors: Graham, S.C. / Wartosch, L. / Gray, S.R. / Scourfield, E.J. / Deane, J.E. / Luzio, J.P. / Owen, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bx9.cif.gz | 512.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bx9.ent.gz | 427.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bx9_validation.pdf.gz | 480.1 KB | Display | wwPDB validaton report |
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Full document | 4bx9_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | 4bx9_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 4bx9_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/4bx9 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/4bx9 | HTTPS FTP |
-Related structure data
Related structure data | 4bx8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN ... , 2 types, 3 molecules ABC
#1: Protein | Mass: 69078.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q96AX1 #2: Protein | | Mass: 11362.010 Da / Num. of mol.: 1 / Fragment: RESIDUES 642-736 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPT3G / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9H269 |
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-Non-polymers , 4 types, 200 molecules
#3: Chemical | #4: Chemical | ChemComp-LMR / ( | #5: Chemical | ChemComp-MLA / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | ADDITIONAL C-TERMINAL RESIDUES ARE DERIVED FROM THE EXPRESSION VECTOR. ADDITIONAL N-TERMINAL ...ADDITIONAL |
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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: 3.64 Å3/Da / Density % sol: 66.19 % / Description: NONE |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: CRYSTALS WERE GROWN IN SITTING DROPS AT 20C. VPS33A:VPS16 COMPLEX (200 NL; A280 = 7.13, APPROX. 8.7 MG/ML) WAS MIXED 1:1 WITH RESERVOIR SOLUTION AND EQUILIBRATED AGAINST 80 UL RESERVOIRS ...Details: CRYSTALS WERE GROWN IN SITTING DROPS AT 20C. VPS33A:VPS16 COMPLEX (200 NL; A280 = 7.13, APPROX. 8.7 MG/ML) WAS MIXED 1:1 WITH RESERVOIR SOLUTION AND EQUILIBRATED AGAINST 80 UL RESERVOIRS CONTAINING 4% TACSIMATE PH 6.0, 12% PEG 3350 (HAMPTON RESEARCH). CRYSTALS WERE CRYOPROTECTED BY BRIEF IMMERSION IN RESERVOIR SOLUTION SUPPLEMENTED WITH 30% ETHYLENE GLYCOL AND CRYO-COOLED BY PLUNGING INTO LIQUID NITROGEN. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2012 / Details: TOROIDAL |
Radiation | Monochromator: SINGLE BOUNCE SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→87.8 Å / Num. obs: 68560 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Biso Wilson estimate: 76.138 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 14 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4BX8 Resolution: 2.6→85.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 15.437 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.302 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.508 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→85.84 Å
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Refine LS restraints |
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