+Open data
-Basic information
Entry | Database: PDB / ID: 8ttd | ||||||
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Title | Structure of VPS29 complexed with Fam21A repeat 21 (1328-1341) | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Vps29 / Fam21 / Retromer / WASH complex / Endosome / endocytosis | ||||||
Function / homology | Function and homology information WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / WASH complex / retromer complex binding / phosphatidylinositol phosphate binding / regulation of Arp2/3 complex-mediated actin nucleation / Golgi to vacuole transport / retromer complex / protein localization to endosome / endocytic recycling ...WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / WASH complex / retromer complex binding / phosphatidylinositol phosphate binding / regulation of Arp2/3 complex-mediated actin nucleation / Golgi to vacuole transport / retromer complex / protein localization to endosome / endocytic recycling / retrograde transport, endosome to Golgi / endosomal transport / intracellular protein transport / protein transport / early endosome membrane / endosome / endosome membrane / early endosome / intracellular membrane-bounded organelle / nucleolus / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.011 Å | ||||||
Authors | Chen, K.-E. / Guo, Q. / Collins, B.M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Structural basis for coupling of the WASH subunit FAM21 with the endosomal SNX27-Retromer complex. Authors: Guo, Q. / Chen, K.E. / Gimenez-Andres, M. / Jellett, A.P. / Gao, Y. / Simonetti, B. / Liu, M. / Danson, C.M. / Heesom, K.J. / Cullen, P.J. / Collins, B.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ttd.cif.gz | 93.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ttd.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ttd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/8ttd ftp://data.pdbj.org/pub/pdb/validation_reports/tt/8ttd | HTTPS FTP |
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-Related structure data
Related structure data | 8ttaC 8ttcC 8tttC 8ttuC 8ttvC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21089.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Vps29 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QZ88 |
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#2: Protein/peptide | Mass: 1494.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q641Q2 |
#3: Chemical | ChemComp-FMT / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M Magnesium Formate, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95365 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95365 Å / Relative weight: 1 |
Reflection | Resolution: 2.01→41.28 Å / Num. obs: 12765 / % possible obs: 99.9 % / Redundancy: 18.8 % / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.013 / Rrim(I) all: 0.053 / Χ2: 0.5 / Net I/σ(I): 25.4 / Num. measured all: 239643 |
Reflection shell | Resolution: 2.01→2.06 Å / % possible obs: 99 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.475 / Num. measured all: 17499 / Num. unique obs: 911 / CC1/2: 0.972 / Rpim(I) all: 0.11 / Rrim(I) all: 0.488 / Χ2: 0.37 / Net I/σ(I) obs: 4.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.011→36.602 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 25.22 / Stereochemistry target values: ML
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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: 2.011→36.602 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -17.9833 Å / Origin y: -3.7482 Å / Origin z: -13.9535 Å
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Refinement TLS group | Selection details: all |