+Open data
-Basic information
Entry | Database: PDB / ID: 6kqp | ||||||
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Title | NSD1 SET domain in complex with SAM | ||||||
Components | Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific | ||||||
Keywords | TRANSFERASE / histone-methyltransferase / SAM complex | ||||||
Function / homology | Function and homology information regulation of RNA polymerase II regulatory region sequence-specific DNA binding / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / histone H3 methyltransferase activity / nuclear thyroid hormone receptor binding / nuclear androgen receptor binding ...regulation of RNA polymerase II regulatory region sequence-specific DNA binding / [histone H3]-lysine36 N-dimethyltransferase / histone H3K36 dimethyltransferase activity / histone H4K20 methyltransferase activity / regulation of peptidyl-serine phosphorylation / histone H3K36 methyltransferase activity / nuclear retinoic acid receptor binding / histone H3 methyltransferase activity / nuclear thyroid hormone receptor binding / nuclear androgen receptor binding / nuclear retinoid X receptor binding / nuclear estrogen receptor binding / transcription coregulator activity / PKMTs methylate histone lysines / transcription corepressor activity / methylation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Cho, H.J. / Cierpicki, T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat.Chem.Biol. / Year: 2020 Title: Covalent inhibition of NSD1 histone methyltransferase. Authors: Huang, H. / Howard, C.A. / Zari, S. / Cho, H.J. / Shukla, S. / Li, H. / Ndoj, J. / Gonzalez-Alonso, P. / Nikolaidis, C. / Abbott, J. / Rogawski, D.S. / Potopnyk, M.A. / Kempinska, K. / Miao, ...Authors: Huang, H. / Howard, C.A. / Zari, S. / Cho, H.J. / Shukla, S. / Li, H. / Ndoj, J. / Gonzalez-Alonso, P. / Nikolaidis, C. / Abbott, J. / Rogawski, D.S. / Potopnyk, M.A. / Kempinska, K. / Miao, H. / Purohit, T. / Henderson, A. / Mapp, A. / Sulis, M.L. / Ferrando, A. / Grembecka, J. / Cierpicki, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kqp.cif.gz | 62.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kqp.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 6kqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kqp_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6kqp_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6kqp_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 6kqp_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kq/6kqp ftp://data.pdbj.org/pub/pdb/validation_reports/kq/6kqp | HTTPS FTP |
-Related structure data
Related structure data | 6kqqC 3ooiS 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
#1: Protein | Mass: 24995.555 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NSD1, ARA267, KMT3B / Production host: Escherichia coli (E. coli) References: UniProt: Q96L73, [histone H3]-lysine36 N-dimethyltransferase | ||||
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#2: Chemical | ChemComp-SAM / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.67 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100mM sodium citrate, pH 5.6, 200mM potassium sodium tartrate, 2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 10515 / % possible obs: 99.5 % / Redundancy: 16.3 % / Rsym value: 0.135 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2.4→2.44 Å / Mean I/σ(I) obs: 2.35 / Num. unique obs: 465 / Rsym value: 0.589 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ooi Resolution: 2.4→45.87 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.106 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.6 Å2 / Biso mean: 49.676 Å2 / Biso min: 9.31 Å2
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Refinement step | Cycle: final / Resolution: 2.4→45.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.401→2.464 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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