+Open data
-Basic information
Entry | Database: PDB / ID: 3mhv | ||||||
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Title | Crystal Structure of Vps4 and Vta1 | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / vps4 / vta1 / AAA / ATPase / ESCRT / MVB / sorting | ||||||
Function / homology | Function and homology information ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission ...ESCRT IV complex / late endosome to lysosome transport via multivesicular body sorting pathway / intralumenal vesicle formation / Endosomal Sorting Complex Required For Transport (ESCRT) / Sealing of the nuclear envelope (NE) by ESCRT-III / protein retention in Golgi apparatus / late endosome to vacuole transport via multivesicular body sorting pathway / sterol metabolic process / nuclear membrane reassembly / midbody abscission / vacuole organization / multivesicular body sorting pathway / membrane fission / plasma membrane repair / late endosome to vacuole transport / multivesicular body assembly / reticulophagy / lipid transport / nucleus organization / endosomal transport / ATPase complex / ATPase activator activity / autophagosome maturation / nuclear pore / multivesicular body / macroautophagy / autophagy / protein-macromolecule adaptor activity / protein transport / midbody / endosome / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | ||||||
Authors | Yang, D. / Hurley, J.H. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structural role of the Vps4-Vta1 interface in ESCRT-III recycling Authors: Yang, D. / Hurley, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mhv.cif.gz | 40.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mhv.ent.gz | 27.2 KB | Display | PDB format |
PDBx/mmJSON format | 3mhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/3mhv ftp://data.pdbj.org/pub/pdb/validation_reports/mh/3mhv | HTTPS FTP |
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-Related 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: 12814.344 Da / Num. of mol.: 1 / Fragment: residues 297-413 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VPS4 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: P52917 |
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#2: Protein/peptide | Mass: 4711.369 Da / Num. of mol.: 1 / Fragment: residues 289-330 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: VTA1 / Plasmid: pGST2 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: Q06263 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.66 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion Details: 16%-24% PEG3350, 0.1-0.3M sodium formate, VAPOR DIFFUSION, temperature 288K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9719 Å |
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Detector | Detector: CCD / Date: Mar 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9719 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. obs: 3803 / % possible obs: 80 % / Redundancy: 3.7 % / Rsym value: 0.085 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 144 / Rsym value: 0.355 / % possible all: 62.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries: 3EIE and 2RKL Resolution: 3.1→37.98 Å / Rfactor Rfree error: 0.025 / Data cutoff high absF: 1127778.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: THe structure was refined also with refmac 5.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 37.0117 Å2 / ksol: 0.272677 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 106.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.1→37.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.29 Å / Rfactor Rfree error: 0.087 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top |