+Open data
-Basic information
Entry | Database: PDB / ID: 7ne3 | ||||||
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Title | Human TET2 in complex with favourable DNA substrate. | ||||||
Components |
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Keywords | OXIDOREDUCTASE / DNA binding / Complex / iron dependent dioxygenase / TET2 / DNA modification / epigenetics / 5-methylcytosine / ion binding / iron binding protein | ||||||
Function / homology | Function and homology information leukocyte differentiation / methylcytosine dioxygenase / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / Specification of primordial germ cells / : / positive regulation of gene expression via chromosomal CpG island demethylation / myeloid cell differentiation / protein O-linked glycosylation ...leukocyte differentiation / methylcytosine dioxygenase / 5-methylcytosine catabolic process / 5-methylcytosine dioxygenase activity / TET1,2,3 and TDG demethylate DNA / Specification of primordial germ cells / : / positive regulation of gene expression via chromosomal CpG island demethylation / myeloid cell differentiation / protein O-linked glycosylation / ferrous iron binding / response to organic cyclic compound / chromosome / cell cycle / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å | ||||||
Authors | Rafalski, D. / Bochtler, M. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function. Authors: Ravichandran, M. / Rafalski, D. / Davies, C.I. / Ortega-Recalde, O. / Nan, X. / Glanfield, C.R. / Kotter, A. / Misztal, K. / Wang, A.H. / Wojciechowski, M. / Razew, M. / Mayyas, I.M. / ...Authors: Ravichandran, M. / Rafalski, D. / Davies, C.I. / Ortega-Recalde, O. / Nan, X. / Glanfield, C.R. / Kotter, A. / Misztal, K. / Wang, A.H. / Wojciechowski, M. / Razew, M. / Mayyas, I.M. / Kardailsky, O. / Schwartz, U. / Zembrzycki, K. / Morison, I.M. / Helm, M. / Weichenhan, D. / Jurkowska, R.Z. / Krueger, F. / Plass, C. / Zacharias, M. / Bochtler, M. / Hore, T.A. / Jurkowski, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ne3.cif.gz | 255.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ne3.ent.gz | 165.9 KB | Display | PDB format |
PDBx/mmJSON format | 7ne3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ne3_validation.pdf.gz | 488.2 KB | Display | wwPDB validaton report |
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Full document | 7ne3_full_validation.pdf.gz | 495.2 KB | Display | |
Data in XML | 7ne3_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 7ne3_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/7ne3 ftp://data.pdbj.org/pub/pdb/validation_reports/ne/7ne3 | HTTPS FTP |
-Related structure data
Related structure data | 7ne6C 4nm6S 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
-Protein / DNA chain , 2 types, 3 molecules ABC
#1: Protein | Mass: 51454.398 Da / Num. of mol.: 1 / Mutation: 0 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TET2, KIAA1546, Nbla00191 / Production host: Escherichia coli (E. coli) / Strain (production host): BL RIL References: UniProt: Q6N021, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor |
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#2: DNA chain | Mass: 3676.431 Da / Num. of mol.: 2 / Mutation: 0 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 6 types, 268 molecules
#3: Chemical | #4: Chemical | ChemComp-FE2 / | #5: Chemical | ChemComp-OGA / | #6: Chemical | #7: Chemical | ChemComp-MES / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.63 Å3/Da / Density % sol: 53.3 % Description: Unit cell: (47.994, 87.711, 260.531, 90, 90, 90) Space group: C 2 2 21 (No. 20) |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.1M MES pH6.3, 23% PEG2000MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→50 Å / Num. obs: 26450 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 51.69 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.0366 / Rrim(I) all: 0.133 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 2.26→2.34 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.571 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2568 / CC1/2: 0.689 / CC star: 0.903 / Rpim(I) all: 0.4525 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4NM6 Resolution: 2.26→43.86 Å / SU ML: 0.3186 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.4677 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.26→43.86 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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