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Yorodumi- PDB-7jyz: Solution NMR structure and dynamics of human Brd3 ET in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jyz | ||||||||||||
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Title | Solution NMR structure and dynamics of human Brd3 ET in complex with MLV IN CTD | ||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Integrase / Brd3 ET / MLV IN CTD | ||||||||||||
Function / homology | Function and homology information host cell late endosome membrane / lncRNA binding / virion assembly / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / host multivesicular body / DNA integration / viral genome integration into host DNA ...host cell late endosome membrane / lncRNA binding / virion assembly / endodermal cell differentiation / protein localization to chromatin / molecular condensate scaffold activity / lysine-acetylated histone binding / host multivesicular body / DNA integration / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / chromatin organization / viral nucleocapsid / DNA recombination / structural constituent of virion / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / chromatin binding / regulation of transcription by RNA polymerase II / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / nucleus / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Moloney murine leukemia virus Homo sapiens (human) | ||||||||||||
Method | SOLUTION NMR / simulated annealing | ||||||||||||
Authors | Aiyer, S. / Liu, G. / Swapna, G.V.T. / Hao, J. / Ma, L.C. / Roth, M.J. / Montelione, G.T. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Structure / Year: 2021 Title: A common binding motif in the ET domain of BRD3 forms polymorphic structural interfaces with host and viral proteins. Authors: Aiyer, S. / Swapna, G.V.T. / Ma, L.C. / Liu, G. / Hao, J. / Chalmers, G. / Jacobs, B.C. / Montelione, G.T. / Roth, M.J. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7jyz.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7jyz.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 7jyz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/7jyz ftp://data.pdbj.org/pub/pdb/validation_reports/jy/7jyz | HTTPS FTP |
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-Related structure data
Related structure data | 7jmyC 7jq8C 7jynC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10131.592 Da / Num. of mol.: 1 / Fragment: C-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moloney murine leukemia virus / Gene: gag-pro-pol / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q8UN00, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H |
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#2: Protein | Mass: 11264.543 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15059 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Details: 20 mM sodium phosphate, 100mM NaCl and 2 mM 2-mercaptoethanol / Ionic strength: 100 mM NaCl mM / Ionic strength err: 0.2 / PH err: 0.05 / Pressure: 1 atm / Pressure err: 0.05 / Temperature: 298 K / Temperature err: 0.1
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 10 | ||||||||||||||||||||||||||||||||||||||||||||
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 |