[English] 日本語
Yorodumi- PDB-2l11: Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l11 | ||||||
---|---|---|---|---|---|---|---|
Title | Solution NMR structure of the Cbx3 in complex with H3K9me3 peptide | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION REGULATOR / chromodomain / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / heterochromatin formation ...chromatin lock complex / histone methyltransferase binding / condensed chromosome, centromeric region / nuclear inner membrane / Transcriptional Regulation by E2F6 / site of DNA damage / chromosome, centromeric region / heterochromatin / pericentric heterochromatin / heterochromatin formation / methylated histone binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription coregulator binding / RNA Polymerase I Promoter Escape / euchromatin / spindle / structural constituent of chromatin / RNA polymerase II transcription regulator complex / rhythmic process / nucleosome / nuclear envelope / chromatin organization / chromosome, telomeric region / chromatin remodeling / protein heterodimerization activity / protein domain specific binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Xenopus laevis (African clawed frog) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Kaustov, L. / Lemak, A. / Fares, C. / Gutmanas, A. / Quang, H. / Loppnau, P. / Min, J. / Edwards, A. / Arrowsmith, C. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Recognition and specificity determinants of the human cbx chromodomains. Authors: Kaustov, L. / Ouyang, H. / Amaya, M. / Lemak, A. / Nady, N. / Duan, S. / Wasney, G.A. / Li, Z. / Vedadi, M. / Schapira, M. / Min, J. / Arrowsmith, C.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2l11.cif.gz | 434.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2l11.ent.gz | 378.7 KB | Display | PDB format |
PDBx/mmJSON format | 2l11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/2l11 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/2l11 | HTTPS FTP |
---|
-Related structure data
Related structure data | 2l12C 2l1bC 3fdtC 3gv6C 3h91C 3i90C 3i91C C: citing same article (ref.) |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 6354.091 Da / Num. of mol.: 1 / Fragment: UNP Residues 29-81 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CBX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon plus RIL / References: UniProt: Q13185 |
---|---|
#2: Protein/peptide | Mass: 1607.877 Da / Num. of mol.: 1 / Fragment: UNP Residues 2-16 / Source method: obtained synthetically / Details: H3K9ME3 15-mer peptide / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: Q92133, UniProt: P84233*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 20 mM sodium phosphate, 200 mM sodium chloride, 2 mM DTT, 1 mM TCEP, 0.5 mM PMSF, 1 mM Benzamidine, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample |
| |||||||||||||||||||||
Sample conditions | Ionic strength: 200 / pH: 7.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |