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Yorodumi- PDB-1h5p: Solution structure of the human Sp100b SAND domain by heteronucle... -
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-Basic information
Entry | Database: PDB / ID: 1h5p | ||||||
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Title | Solution structure of the human Sp100b SAND domain by heteronuclear NMR. | ||||||
Components | NUCLEAR AUTOANTIGEN SP100-B | ||||||
Keywords | NUCLEAR PROTEIN / TRANSCRIPTION / DNA BINDING / SP100B / SAND DOMAIN / KDWK / ANTIGEN / ALTERNATIVE SPLICING | ||||||
Function / homology | Function and homology information regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / regulation of extrinsic apoptotic signaling pathway via death domain receptors / type I interferon-mediated signaling pathway / response to type II interferon ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / negative regulation of endothelial cell migration / regulation of extrinsic apoptotic signaling pathway via death domain receptors / type I interferon-mediated signaling pathway / response to type II interferon / negative regulation of DNA binding / DNA damage response, signal transduction by p53 class mediator / retinoic acid receptor signaling pathway / regulation of angiogenesis / SUMOylation of DNA damage response and repair proteins / type II interferon-mediated signaling pathway / response to retinoic acid / telomere maintenance / nuclear periphery / response to cytokine / negative regulation of DNA-binding transcription factor activity / PML body / kinase binding / positive regulation of DNA-binding transcription factor activity / Interferon gamma signaling / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / protein dimerization activity / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / negative regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / ARIA AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS | ||||||
Authors | Bottomley, M.J. / Liu, Z. / Collard, M.W. / Huggenvik, J.I. / Gibson, T.J. / Sattler, M. | ||||||
Citation | Journal: Nat. Struct. Biol. / Year: 2001 Title: The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation. Authors: Bottomley, M.J. / Collard, M.W. / Huggenvik, J.I. / Liu, Z. / Gibson, T.J. / Sattler, M. #1: Journal: J.Biol.Chem. / Year: 1999 Title: Nuclear Deaf-1-Related (Nudr) Protein Contains a Novel DNA Binding Domain and Represses Transcription of the Heterogeneous Nuclear Ribonucleoprotein A2/B1 Promoter Authors: Michelson, R.J. / Collard, M.W. / Ziemba, A.J. / Persinger, J. / Bartholomew, B. / Huggenvik, J.I. #2: Journal: Trends Biochem.Sci. / Year: 1998 Title: The Apeced Polyglandular Autoimmune Syndrome Protein, Aire-1, Contains the Sand Domain and is Probably a Transcription Factor Authors: Gibson, T.J. / Ramu, C. / Gemuend, C. / Aasland, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h5p.cif.gz | 340.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h5p.ent.gz | 298 KB | Display | PDB format |
PDBx/mmJSON format | 1h5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h5/1h5p ftp://data.pdbj.org/pub/pdb/validation_reports/h5/1h5p | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 11052.805 Da / Num. of mol.: 1 / Fragment: RESIDUES 595-688 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MODIFIED PET-24D Gene (production host): EXPRESSED AS FUSION PROTEIN WITH N-TERMINAL 6-HISTIDINE TAG AND A TEV PROTEASE CLEAVAGE SITE Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23497 |
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Sequence details | THE STRUCTURE IS FOR THE SPLICE VARIANT SP100B SAND DOMAIN. THE RESIDUES 685 -688 (RILE IN ISOFORM ...THE STRUCTURE IS FOR THE SPLICE VARIANT SP100B SAND DOMAIN. THE RESIDUES 685 -688 (RILE IN ISOFORM SP100-A) ARE (VTIK IN ISOFORM SP100-B) DIFFERENT IN THE TWO SPLICE VARIANTS MET A 594 IS A CLONING ARTIFACT. |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.2 MM PROTEIN, 20 MM SODIUM PHOSPHATE PH 6.5, 50 MM NACL, 4 MM DTT |
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Sample conditions | Ionic strength: 20 MM SODIUM PHOSPHATE, 50 MM SODIUM CHLORIDE pH: 6.5 / Pressure: 1 atm / Temperature: 295.0 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: ARIA AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS Software ordinal: 1 Details: DURING THE STRUCTURE CALCULATIONS, THE PROGRAM ARIA 1.0 (M.NILGES & S.I.O'DONOGHUE) WAS USED TO EMPLOY DISTANCE RESTRAINTS DERIVED FROM AMBIGUOUSLY ASSIGNED NOES. FROM A TOTAL OF 2120 NOES, ...Details: DURING THE STRUCTURE CALCULATIONS, THE PROGRAM ARIA 1.0 (M.NILGES & S.I.O'DONOGHUE) WAS USED TO EMPLOY DISTANCE RESTRAINTS DERIVED FROM AMBIGUOUSLY ASSIGNED NOES. FROM A TOTAL OF 2120 NOES, ABOUT 80% WERE MANUALLY ASSIGNED, THE REMAINDER WAS ASSIGNED BY ARIA. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: ACCEPTABLE COVALENT GEOMETRY, FAVOURABLE NON-BOND ENERGY, FEWEST RESTRAINT VIOLATIONS, LOWEST OVERALL ENERGIES Conformers calculated total number: 100 / Conformers submitted total number: 10 |