+Open data
-Basic information
Entry | Database: PDB / ID: 7evr | ||||||
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Title | Crystal structure of hnRNP L RRM2 in complex with SETD2 | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / complex | ||||||
Function / homology | Function and homology information mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / ribonucleoprotein granule / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis ...mesoderm morphogenesis / coronary vasculature morphogenesis / morphogenesis of a branching structure / peptidyl-lysine trimethylation / ribonucleoprotein granule / cell migration involved in vasculogenesis / microtubule cytoskeleton organization involved in mitosis / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / embryonic placenta morphogenesis / regulation of mRNA export from nucleus / pericardium development / stem cell development / nucleosome organization / histone H3K36 methyltransferase activity / protein-lysine N-methyltransferase activity / response to type I interferon / positive regulation of ossification / embryonic cranial skeleton morphogenesis / response to alkaloid / regulation of protein localization to chromatin / response to metal ion / histone H3 methyltransferase activity / regulation of double-strand break repair via homologous recombination / endodermal cell differentiation / regulation of alternative mRNA splicing, via spliceosome / regulation of RNA splicing / Processing of Capped Intron-Containing Pre-mRNA / alpha-tubulin binding / positive regulation of interferon-alpha production / RNA processing / mismatch repair / positive regulation of autophagy / pre-mRNA intronic binding / forebrain development / mRNA Splicing - Major Pathway / Transferases; Transferring one-carbon groups; Methyltransferases / regulation of cytokinesis / neural tube closure / transcription elongation by RNA polymerase II / stem cell differentiation / response to organic cyclic compound / mRNA processing / PKMTs methylate histone lysines / chromosome / regulation of gene expression / angiogenesis / defense response to virus / transcription cis-regulatory region binding / ribonucleoprotein complex / negative regulation of DNA-templated transcription / mRNA binding / regulation of DNA-templated transcription / chromatin / RNA binding / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Li, F.D. / Wang, S.M. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing. Authors: Bhattacharya, S. / Wang, S. / Reddy, D. / Shen, S. / Zhang, Y. / Zhang, N. / Li, H. / Washburn, M.P. / Florens, L. / Shi, Y. / Workman, J.L. / Li, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7evr.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7evr.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 7evr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7evr_validation.pdf.gz | 431 KB | Display | wwPDB validaton report |
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Full document | 7evr_full_validation.pdf.gz | 431 KB | Display | |
Data in XML | 7evr_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 7evr_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/7evr ftp://data.pdbj.org/pub/pdb/validation_reports/ev/7evr | HTTPS FTP |
-Related structure data
Related structure data | 7evsC 3zzyS 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: 12626.244 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HNRNPL, HNRPL, P/OKcl.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P14866 #2: Protein/peptide | Mass: 2788.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) References: UniProt: Q9BYW2, [histone H3]-lysine36 N-trimethyltransferase, Transferases; Transferring one-carbon groups; Methyltransferases #3: 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: 2.42 Å3/Da / Density % sol: 49.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.8M Potassium/Sodium phosphate, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→40 Å / Num. obs: 27697 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.64 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.06 / Rrim(I) all: 0.141 / Χ2: 1.024 / Net I/σ(I): 4.6 / Num. measured all: 142925 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZZY Resolution: 1.8→39.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.54 / 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 max: 54.19 Å2 / Biso mean: 19.619 Å2 / Biso min: 7.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→39.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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