+Open data
-Basic information
Entry | Database: PDB / ID: 5t8l | ||||||
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Title | Crystal structure of Snf7 under 350 MPa | ||||||
Components | Vacuolar-sorting protein SNF7 | ||||||
Keywords | PROTEIN TRANSPORT / Snf7 / high-pressure cryocooling / resolution | ||||||
Function / homology | Function and homology information ESCRT III complex assembly / intralumenal vesicle formation / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / late endosome to vacuole transport ...ESCRT III complex assembly / intralumenal vesicle formation / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / Macroautophagy / ATP export / ESCRT III complex / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / late endosome to vacuole transport / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / reticulophagy / multivesicular body / cytoplasmic side of plasma membrane / protein transport / nuclear envelope / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Huang, Q. / Szebenyi, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of Snf7 under 350 MPa Authors: Huang, Q. / Szebenyi, D. #1: Journal: Elife / Year: 2015 Title: Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments. Authors: Tang, S. / Henne, W.M. / Borbat, P.P. / Buchkovich, N.J. / Freed, J.H. / Mao, Y. / Fromme, J.C. / Emr, S.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5t8l.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5t8l.ent.gz | 46.3 KB | Display | PDB format |
PDBx/mmJSON format | 5t8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t8/5t8l ftp://data.pdbj.org/pub/pdb/validation_reports/t8/5t8l | HTTPS FTP |
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-Related structure data
Related structure data | 5fd9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15803.133 Da / Num. of mol.: 1 / Fragment: UNP residues 12-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SNF7, DID1, VPS32, YLR025W / Production host: Escherichia coli (E. coli) / References: UniProt: P39929 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 38.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 6% PEG20000, 110 mM NaCl, 70 mM Mes pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 6489 / % possible obs: 99.1 % / Redundancy: 3.2 % / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.365 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5fd9 Resolution: 2.2→32.69 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 29.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→32.69 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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