+Open data
-Basic information
Entry | Database: PDB / ID: 5gnr | |||||||||
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Title | the structure of mini-MFN1 K88A in complex with GDP | |||||||||
Components | Mitofusin-1 | |||||||||
Keywords | HYDROLASE / Mitofusin 1 / Bdlp-like fold / fusion | |||||||||
Function / homology | Function and homology information RHOT2 GTPase cycle / outer mitochondrial membrane protein complex / mitochondrion localization / GTP metabolic process / positive regulation of mitochondrial membrane potential / mitochondrial fusion / PINK1-PRKN Mediated Mitophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane ...RHOT2 GTPase cycle / outer mitochondrial membrane protein complex / mitochondrion localization / GTP metabolic process / positive regulation of mitochondrial membrane potential / mitochondrial fusion / PINK1-PRKN Mediated Mitophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane / GTPase activity / GTP binding / mitochondrion / membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Yan, L. / Yu, C. / Ming, Z. / Lou, Z. / Rao, Z. / Hu, J. | |||||||||
Funding support | China, Armenia, 2items
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Citation | Journal: To Be Published Title: BDLP-like folding of Mitofusin 1 Authors: Qi, Y. / Yan, L. / Yu, C. / Lou, Z. / Rao, Z. / Hu, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gnr.cif.gz | 92.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gnr.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 5gnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/5gnr ftp://data.pdbj.org/pub/pdb/validation_reports/gn/5gnr | 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: 47334.785 Da / Num. of mol.: 1 / Fragment: UNP residues 1-364 / Mutation: K88A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MFN1 / Production host: Escherichia coli (E. coli) References: UniProt: Q8IWA4, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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#2: Chemical | ChemComp-GDP / Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Fragment: UNP residues 1-364 / Mutation: K88A Source method: isolated from a genetically manipulated source Formula: C10H15N5O11P2 References: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement Comment: GDP, energy-carrying molecule*YM |
#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: 2.67 Å3/Da / Density % sol: 53.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 200 mM ammonium fluoride, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9785 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→50 Å / Num. obs: 15269 / % possible obs: 99.8 % / Redundancy: 7.8 % / Net I/σ(I): 21.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→39.959 Å / SU ML: 0.35 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 31.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→39.959 Å
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Refine LS restraints |
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LS refinement shell |
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