+Open data
-Basic information
Entry | Database: PDB / ID: 6jfl | ||||||
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Title | Nucleotide-free Mitofusin2 (MFN2) | ||||||
Components | Mitofusin-2,cDNA FLJ57997, highly similar to Transmembrane GTPase MFN2 | ||||||
Keywords | MEMBRANE PROTEIN / mitochondriral fusion / GTPase activity / CMT2A | ||||||
Function / homology | Function and homology information RHOT2 GTPase cycle / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / mitochondrion localization / protein localization to phagophore assembly site / camera-type eye morphogenesis / protein targeting to mitochondrion / blastocyst formation / negative regulation of Ras protein signal transduction / mitochondrial membrane organization / mitochondrial fusion ...RHOT2 GTPase cycle / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / mitochondrion localization / protein localization to phagophore assembly site / camera-type eye morphogenesis / protein targeting to mitochondrion / blastocyst formation / negative regulation of Ras protein signal transduction / mitochondrial membrane organization / mitochondrial fusion / positive regulation of vascular associated smooth muscle cell apoptotic process / response to unfolded protein / aerobic respiration / positive regulation of vascular associated smooth muscle cell proliferation / PINK1-PRKN Mediated Mitophagy / negative regulation of smooth muscle cell proliferation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule cytoskeleton / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane / GTPase activity / apoptotic process / ubiquitin protein ligase binding / GTP binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.806 Å | ||||||
Authors | Li, Y.J. / Cao, Y.L. / Feng, J.X. / Qi, Y.B. / Meng, S.X. / Yang, J.F. / Zhong, Y.T. / Kang, S.S. / Chen, X.X. / Lan, L. ...Li, Y.J. / Cao, Y.L. / Feng, J.X. / Qi, Y.B. / Meng, S.X. / Yang, J.F. / Zhong, Y.T. / Kang, S.S. / Chen, X.X. / Lan, L. / Luo, L. / Yu, B. / Chen, S.D. / Chan, D.C. / Hu, J.J. / Gao, S. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural insights of human mitofusin-2 into mitochondrial fusion and CMT2A onset. Authors: Li, Y.J. / Cao, Y.L. / Feng, J.X. / Qi, Y. / Meng, S. / Yang, J.F. / Zhong, Y.T. / Kang, S. / Chen, X. / Lan, L. / Luo, L. / Yu, B. / Chen, S. / Chan, D.C. / Hu, J. / Gao, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jfl.cif.gz | 665.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jfl.ent.gz | 549.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/6jfl ftp://data.pdbj.org/pub/pdb/validation_reports/jf/6jfl | HTTPS FTP |
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-Related structure data
Related structure data | 6jfkC 6jfmSC 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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Unit cell |
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-Components
#1: Protein | Mass: 49830.523 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MFN2, CPRP1, KIAA0214 / Production host: Escherichia coli (E. coli) References: UniProt: O95140, UniProt: B7Z3H8, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.43 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.19 M Calcium chloride 0.095 M HEPES PH7.5 26.6% (V/V) PEG400 5% (V/V) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.7 Å / Num. obs: 44958 / % possible obs: 98 % / Redundancy: 3.3 % / Rrim(I) all: 0.128 / Rsym value: 0.106 / Net I/σ(I): 10.42 |
Reflection shell | Resolution: 2.81→2.98 Å / Num. unique obs: 6966 / Rrim(I) all: 0.586 / Rsym value: 0.49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JFM Resolution: 2.806→36.337 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 34.23
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.806→36.337 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: 8.232 Å / Origin y: 12.6275 Å / Origin z: 34.8832 Å
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Refinement TLS group | Selection details: all |