+Open data
-Basic information
Entry | Database: PDB / ID: 6jfk | ||||||
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Title | GDP bound 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 / 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 ...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 / positive regulation of cold-induced thermogenesis / 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 / ubiquitin protein ligase binding / GTP binding / apoptotic process / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.997 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 | 6jfk.cif.gz | 193.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jfk.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 6jfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jfk_validation.pdf.gz | 836.3 KB | Display | wwPDB validaton report |
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Full document | 6jfk_full_validation.pdf.gz | 842.7 KB | Display | |
Data in XML | 6jfk_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6jfk_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/6jfk ftp://data.pdbj.org/pub/pdb/validation_reports/jf/6jfk | HTTPS FTP |
-Related structure data
Related structure data | 6jflC 6jfmC 5gomS 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: 49830.523 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | ChemComp-GDP / | ||
#3: Chemical | ChemComp-CIT / | ||
#4: Chemical | ChemComp-GOL / #5: 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: 2.4 Å3/Da / Density % sol: 48.69 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium citrate tribasic tetrahydrate, 35% (V/V) Glycerol ethoxylate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 1.997→49.6 Å / Num. obs: 34454 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rrim(I) all: 0.064 / Rsym value: 0.058 / Net I/σ(I): 18.31 |
Reflection shell | Resolution: 2→2.12 Å / Num. unique obs: 5321 / Rpim(I) all: 0.52 / Rsym value: 0.475 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GOM Resolution: 1.997→49.223 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.37 / Phase error: 19.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.997→49.223 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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