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Yorodumi- PDB-8jnr: Crystal structure of human ALKBH3 bound to 3mC containing ssDNA t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jnr | ||||||
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Title | Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / RNA m1A demethylase / DNA BINDING PROTEIN-DNA COMPLEX | ||||||
Function / homology | Function and homology information mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair ...mRNA N1-methyladenine demethylase / mRNA N1-methyladenosine dioxygenase activity / ALKBH3 mediated reversal of alkylation damage / DNA oxidative demethylase / : / : / : / oxidative RNA demethylase activity / broad specificity oxidative DNA demethylase activity / DNA alkylation repair / L-ascorbic acid binding / ferrous iron binding / cell population proliferation / DNA repair / mitochondrion / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.66 Å | ||||||
Authors | Zhang, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024 Title: The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation. Authors: Zhang, L. / Duan, H.C. / Paduch, M. / Hu, J. / Zhang, C. / Mu, Y. / Lin, H. / He, C. / Kossiakoff, A.A. / Jia, G. / Zhang, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jnr.cif.gz | 495.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jnr.ent.gz | 400.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jnr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jn/8jnr ftp://data.pdbj.org/pub/pdb/validation_reports/jn/8jnr | HTTPS FTP |
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-Related structure data
Related structure data | 8jnkC 2uiwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 8 molecules GHIJKLMN
#3: Antibody | Mass: 22927.537 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #4: Antibody | Mass: 23667.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
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-Protein / DNA chain , 2 types, 6 molecules ACDEBF
#1: Protein | Mass: 27693.117 Da / Num. of mol.: 4 / Mutation: D110S, D189C, C201S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALKBH3, ABH3 / Production host: Escherichia coli (E. coli) References: UniProt: Q96Q83, DNA oxidative demethylase, mRNA N1-methyladenine demethylase #2: DNA chain | Mass: 867.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 3 types, 7 molecules
#5: Chemical | #6: Chemical | ChemComp-MN / #7: Chemical | ChemComp-ME6 / [( | |
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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: 3.1 Å3/Da / Density % sol: 60.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1M NaCl, 20% PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9875 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.66→50 Å / Num. obs: 35958 / % possible obs: 89.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.244 / Χ2: 1.499 / Net I/σ(I): 5.2 / Num. measured all: 97662 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2UIW Resolution: 3.66→34.38 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9 / Stereochemistry target values: ML
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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: 84.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.66→34.38 Å
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LS refinement shell |
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