+Open data
-Basic information
Entry | Database: PDB / ID: 6jfm | ||||||
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Title | Mitofusin2 (MFN2)_T111D | ||||||
Components | Mitofusin-2,Mitofusin-2 | ||||||
Keywords | MEMBRANE PROTEIN / mitochondriral fusion / GTPase activity / CMT2A | ||||||
Function / homology | Function and homology information : / RHOT2 GTPase cycle / type 2 mitophagy / mitochondrion localization / camera-type eye morphogenesis / protein localization to phagophore assembly site / protein targeting to mitochondrion / negative regulation of Ras protein signal transduction / blastocyst formation / mitochondrial membrane organization ...: / RHOT2 GTPase cycle / type 2 mitophagy / mitochondrion localization / camera-type eye morphogenesis / protein localization to phagophore assembly site / protein targeting to mitochondrion / negative regulation of Ras protein signal transduction / blastocyst formation / mitochondrial membrane organization / mitochondrial fusion / positive regulation of vascular associated smooth muscle cell apoptotic process / response to unfolded protein / positive regulation of vascular associated smooth muscle cell proliferation / aerobic respiration / PINK1-PRKN Mediated Mitophagy / negative regulation of smooth muscle cell proliferation / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of cold-induced thermogenesis / Factors involved in megakaryocyte development and platelet production / mitochondrial outer membrane / membrane => GO:0016020 / GTPase activity / ubiquitin protein ligase binding / GTP binding / apoptotic process / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Macaca mulatta (Rhesus monkey) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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 | 6jfm.cif.gz | 360.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jfm.ent.gz | 292.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jfm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jfm_validation.pdf.gz | 458.8 KB | Display | wwPDB validaton report |
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Full document | 6jfm_full_validation.pdf.gz | 472.7 KB | Display | |
Data in XML | 6jfm_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 6jfm_validation.cif.gz | 48.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/6jfm ftp://data.pdbj.org/pub/pdb/validation_reports/jf/6jfm | HTTPS FTP |
-Related structure data
Related structure data | 6jfkSC 6jflC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49844.508 Da / Num. of mol.: 2 / Mutation: T111D,T111D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Macaca mulatta (Rhesus monkey) Gene: MFN2, CPRP1, KIAA0214, MFN2, EGK_00242 / Production host: Escherichia coli (E. coli) References: UniProt: O95140, UniProt: G7MGV9, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement #2: Chemical | #3: Chemical | #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: 2.2 Å3/Da / Density % sol: 44.16 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.16 M Calcium acetate 0.08 M Sodium cacodylate PH 6.5 14.4% (W/V) PEG 8000 20% (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: 0.97914 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97914 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→126.6 Å / Num. obs: 50379 / % possible obs: 98.8 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.09 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.09→2.14 Å / Rmerge(I) obs: 0.573 / Num. unique obs: 3741 / Rrim(I) all: 0.743 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JFK Resolution: 2.09→31.641 Å / SU ML: 0.23 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 24.57
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.09→31.641 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: -7.2694 Å / Origin y: -12.3214 Å / Origin z: 16.5388 Å
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Refinement TLS group | Selection details: all |