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Yorodumi- PDB-2kft: NMR Solution structure of the first PHD finger domain of human Au... -
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-Basic information
Entry | Database: PDB / ID: 2kft | ||||||
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Title | NMR Solution structure of the first PHD finger domain of human Autoimmune Regulator (AIRE) in complex with Histone H3(1-20Cys) Peptide | ||||||
Components |
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Keywords | TRANSCRIPTION/PROTEIN BINDING / PHD Finger / Histone Code / AIRE / APECED / Transcription / Alternative splicing / Cytoplasm / Disease mutation / DNA-binding / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Transcription regulation / Zinc / Zinc-finger / Chromosomal protein / Nucleosome core / TRANSCRIPTION-PROTEIN BINDING COMPLEX | ||||||
Function / homology | Function and homology information peripheral T cell tolerance induction / central tolerance induction to self antigen / regulation of thymocyte migration / thymus epithelium morphogenesis / negative thymic T cell selection / female germ cell nucleus / humoral immune response / translation regulator activity / positive regulation of chemokine production / male germ cell nucleus ...peripheral T cell tolerance induction / central tolerance induction to self antigen / regulation of thymocyte migration / thymus epithelium morphogenesis / negative thymic T cell selection / female germ cell nucleus / humoral immune response / translation regulator activity / positive regulation of chemokine production / male germ cell nucleus / RNA polymerase II transcription regulatory region sequence-specific DNA binding / histone binding / transcription by RNA polymerase II / nuclear body / immune response / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / zinc ion binding / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 20 | ||||||
Authors | Chakravarty, S. / Zeng, L. / Zhou, M. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structure and Site-Specific Recognition of Histone H3 by the PHD Finger of Human Autoimmune Regulator. Authors: Chakravarty, S. / Zeng, L. / Zhou, M.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kft.cif.gz | 449.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kft.ent.gz | 372.3 KB | Display | PDB format |
PDBx/mmJSON format | 2kft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kft_validation.pdf.gz | 351.6 KB | Display | wwPDB validaton report |
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Full document | 2kft_full_validation.pdf.gz | 581.6 KB | Display | |
Data in XML | 2kft_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 2kft_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/2kft ftp://data.pdbj.org/pub/pdb/validation_reports/kf/2kft | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 6019.827 Da / Num. of mol.: 1 / Fragment: AIRE PHD-type 1 Zinc Finger Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AIRE, APECED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43918 |
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#2: Protein/peptide | Mass: 2293.715 Da / Num. of mol.: 1 / Fragment: Histone H3 1-20Cys N-terminal domain / Source method: obtained synthetically |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: NMR Structure of AIRE PHD Finger in Complex with unmodified Histone H3 1-20 N-terminal tail | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-100% 15N] AIRE PHD finger 1, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.5 mM / Component: AIRE PHD finger 1 / Isotopic labeling: [U-100% 15N] |
Sample conditions | Ionic strength: 250 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |