+Open data
-Basic information
Entry | Database: PDB / ID: 5mtv | ||||||
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Title | Active structure of EHD4 complexed with ATP-gamma-S | ||||||
Components | EH domain-containing protein 4 | ||||||
Keywords | ENDOCYTOSIS / dynamin-like / membrane protein / auto-inhibition / activation | ||||||
Function / homology | Function and homology information pinocytosis / endocytic recycling / regulation of endocytosis / cilium assembly / endocytic vesicle / protein localization to plasma membrane / protein homooligomerization / cellular response to growth factor stimulus / endocytosis / recycling endosome membrane ...pinocytosis / endocytic recycling / regulation of endocytosis / cilium assembly / endocytic vesicle / protein localization to plasma membrane / protein homooligomerization / cellular response to growth factor stimulus / endocytosis / recycling endosome membrane / positive regulation of peptidyl-tyrosine phosphorylation / early endosome membrane / early endosome / calcium ion binding / GTP binding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | ||||||
Authors | Melo, A.A. / Daumke, O. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: Structural insights into the activation mechanism of dynamin-like EHD ATPases. Authors: Melo, A.A. / Hegde, B.G. / Shah, C. / Larsson, E. / Isas, J.M. / Kunz, S. / Lundmark, R. / Langen, R. / Daumke, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mtv.cif.gz | 241.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mtv.ent.gz | 198.3 KB | Display | PDB format |
PDBx/mmJSON format | 5mtv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/5mtv ftp://data.pdbj.org/pub/pdb/validation_reports/mt/5mtv | HTTPS FTP |
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-Related structure data
Related structure data | 5mvfC 4cidS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 59488.074 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ehd4, Past2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EQP2 |
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#2: Chemical | ChemComp-AGS / |
#3: Chemical | ChemComp-MG / |
#4: 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: 3.5 Å3/Da / Density % sol: 64.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Sodium polyacrylate 5100, magnesium chloride, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2015 / Details: DOUBLE MIRROR |
Radiation | Monochromator: double Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→48.5 Å / Num. obs: 21733 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 64.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.035 / Rsym value: 0.088 / Net I/σ(I): 19.04 |
Reflection shell | Resolution: 2.79→2.96 Å / Redundancy: 7.65 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 3412 / CC1/2: 0.69 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4CID Resolution: 2.79→48.5 Å / SU ML: 0.45 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 25.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.316 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→48.5 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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