+Open data
-Basic information
Entry | Database: PDB / ID: 4u7i | ||||||
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Title | Structure of the complex of Spartin MIT and IST1 MIM | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / Complex / MIM3 | ||||||
Function / homology | Function and homology information negative regulation of collateral sprouting in absence of injury / viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / lipid droplet organization ...negative regulation of collateral sprouting in absence of injury / viral capsid secondary envelopment / MIT domain binding / abscission / ESCRT III complex disassembly / cytoskeleton-dependent cytokinesis / collateral sprouting / Sealing of the nuclear envelope (NE) by ESCRT-III / positive regulation of collateral sprouting / lipid droplet organization / multivesicular body assembly / collateral sprouting in absence of injury / Flemming body / neuromuscular process / positive regulation of proteolysis / viral release from host cell / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of BMP signaling pathway / adipose tissue development / BMP signaling pathway / lipid droplet / regulation of mitochondrial membrane potential / establishment of protein localization / protein localization / azurophil granule lumen / protein transport / nuclear envelope / midbody / mitochondrial outer membrane / cadherin binding / protein domain specific binding / cell division / intracellular membrane-bounded organelle / centrosome / synapse / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / chromatin / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.794 Å | ||||||
Authors | Guo, E.Z. / Xu, Z. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Distinct Mechanisms of Recognizing Endosomal Sorting Complex Required for Transport III (ESCRT-III) Protein IST1 by Different Microtubule Interacting and Trafficking (MIT) Domains. Authors: Guo, E.Z. / Xu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4u7i.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4u7i.ent.gz | 44.5 KB | Display | PDB format |
PDBx/mmJSON format | 4u7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4u7i_validation.pdf.gz | 417.1 KB | Display | wwPDB validaton report |
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Full document | 4u7i_full_validation.pdf.gz | 417.1 KB | Display | |
Data in XML | 4u7i_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 4u7i_validation.cif.gz | 9.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u7/4u7i ftp://data.pdbj.org/pub/pdb/validation_reports/u7/4u7i | HTTPS FTP |
-Related structure data
Related structure data | 4u7eC 4u7yC 2dl1S C: citing same article (ref.) 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10794.293 Da / Num. of mol.: 1 / Fragment: MIT domain (UNP residues 8-101) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPG20, KIAA0610, TAHCCP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q8N0X7 |
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#2: Protein/peptide | Mass: 3009.262 Da / Num. of mol.: 1 / Fragment: UNP residues 341-364 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IST1, KIAA0174 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P53990 |
#3: 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: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 2.9 M Na-malonate / PH range: 6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97828 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97828 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→29.61 Å / Num. obs: 12400 / % possible obs: 99.6 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 43 |
Reflection shell | Redundancy: 8.4 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 4 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DL1 Resolution: 1.794→29.61 Å / SU ML: 0.19 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.94 / 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: 1.794→29.61 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: -12.3844 Å / Origin y: 6.1248 Å / Origin z: -7.1335 Å
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Refinement TLS group | Selection details: all |