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Yorodumi- PDB-2ysm: Solution structure of the second and third PHD domain from Histon... -
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-Basic information
Entry | Database: PDB / ID: 2ysm | ||||||
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Title | Solution structure of the second and third PHD domain from Histone-lysine N-methyltransferase 2C (KMT2C/MLL3) | ||||||
Components | Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog | ||||||
Keywords | TRANSFERASE / PHD domain / Myeloid/lymphoid or mixed-lineage leukemia protein / Histone-lysine N-methyltransferase / H3 lysine-4 specific MLL3 / Homologous to ALR protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / acyltransferase activity / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes / response to electrical stimulus ...[histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / histone H3K4 trimethyltransferase activity / MLL3/4 complex / histone H3K4 methyltransferase activity / histone methyltransferase complex / acyltransferase activity / histone methyltransferase activity / Formation of WDR5-containing histone-modifying complexes / response to electrical stimulus / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / PKMTs methylate histone lysines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone binding / methylation / transcription coactivator activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Qin, X.R. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the first and second PHD domain from Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog Authors: Qin, X.R. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ysm.cif.gz | 618 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ysm.ent.gz | 514.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ysm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ysm_validation.pdf.gz | 344.6 KB | Display | wwPDB validaton report |
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Full document | 2ysm_full_validation.pdf.gz | 492.1 KB | Display | |
Data in XML | 2ysm_validation.xml.gz | 38.3 KB | Display | |
Data in CIF | 2ysm_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ys/2ysm ftp://data.pdbj.org/pub/pdb/validation_reports/ys/2ysm | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11879.634 Da / Num. of mol.: 1 / Fragment: PHD domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MLL3, HALR, KIAA1506 / Plasmid: P070115-52 / Production host: cell-free protein synthesis (unknown) References: UniProt: Q8NEZ4, histone-lysine N-methyltransferase |
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#2: Chemical | ChemComp-ZN / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: spectrometer_id 1 for 3D_15N_separaed_NOESY; spectrometer_id 2 for 3D_13C_separaed_NOESY; |
-Sample preparation
Details | Contents: 0.94mM 13C, 15N-labeled protein; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZnCl2+1mM IDA; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |