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- PDB-1h5p: Solution structure of the human Sp100b SAND domain by heteronucle... -

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Basic information

Entry
Database: PDB / ID: 1h5p
TitleSolution structure of the human Sp100b SAND domain by heteronuclear NMR.
ComponentsNUCLEAR AUTOANTIGEN SP100-B
KeywordsNUCLEAR 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 / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / regulation of angiogenesis ...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 / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / type I interferon-mediated signaling pathway / regulation of angiogenesis / response to type II interferon / response to retinoic acid / type II interferon-mediated signaling pathway / SUMOylation of DNA damage response and repair proteins / retinoic acid receptor signaling pathway / response to cytokine / telomere maintenance / nuclear periphery / DNA damage response, signal transduction by p53 class mediator / PML body / kinase binding / Interferon gamma signaling / transcription corepressor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / protein dimerization activity / nuclear body / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / 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
SAND domain-like / SAND domain / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain ...SAND domain-like / SAND domain / HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Nuclear autoantigen Sp-100
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA AMBIGUOUS DISTANCE RESTRAINTS SIMULATED ANNEALING WITH TORSION ANGLE DYNAMICS
AuthorsBottomley, 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
DepositionMay 24, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: NUCLEAR AUTOANTIGEN SP100-B


Theoretical massNumber of molelcules
Total (without water)11,0531
Polymers11,0531
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100ACCEPTABLE COVALENT GEOMETRY, FAVOURABLE NON-BOND ENERGY, FEWEST RESTRAINT VIOLATIONS, LOWEST OVERALL ENERGIES
RepresentativeModel #1

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Components

#1: Protein NUCLEAR AUTOANTIGEN SP100-B / SAND DOMAIN / KDWK DOMAIN / SPECKLED 100 KDA / NUCLEAR DOT-ASSOCIATED SP100 PROTEIN / LYSP100B


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
Sequence detailsTHE 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.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-SEPARATED NOESY
1213D 15N-SEPARATED NOESY
131HNHA

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Sample preparation

DetailsContents: 1.2 MM PROTEIN, 20 MM SODIUM PHOSPHATE PH 6.5, 50 MM NACL, 4 MM DTT
Sample conditionsIonic 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

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DRXBrukerDRX7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS0.3BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
NMRPipestructure solution
XEASYstructure solution
ARIA1structure solution
CNS0.9structure solution
RefinementMethod: 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 ensembleConformer 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

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