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- PDB-1nfa: HUMAN TRANSCRIPTION FACTOR NFATC DNA BINDING DOMAIN, NMR, 10 STRU... -

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Basic information

Entry
Database: PDB / ID: 1nfa
TitleHUMAN TRANSCRIPTION FACTOR NFATC DNA BINDING DOMAIN, NMR, 10 STRUCTURES
ComponentsHUMAN TRANSCRIPTION FACTOR NFATC1
KeywordsTRANSCRIPTION REGULATION / NFAT / REL-HOMOLOGY FOLD / ACTIVATES CYTOKINE TRANSCRIPTION
Function / homology
Function and homology information


skeletal muscle adaptation / negative regulation of vascular associated smooth muscle cell differentiation / mononuclear cell differentiation / calcineurin-NFAT signaling cascade / pulmonary valve morphogenesis / aortic valve morphogenesis / response to muscle activity / positive regulation of DNA biosynthetic process / CLEC7A (Dectin-1) induces NFAT activation / FK506 binding ...skeletal muscle adaptation / negative regulation of vascular associated smooth muscle cell differentiation / mononuclear cell differentiation / calcineurin-NFAT signaling cascade / pulmonary valve morphogenesis / aortic valve morphogenesis / response to muscle activity / positive regulation of DNA biosynthetic process / CLEC7A (Dectin-1) induces NFAT activation / FK506 binding / mitogen-activated protein kinase p38 binding / negative regulation of Wnt signaling pathway / Calcineurin activates NFAT / sarcoplasm / cellular response to transforming growth factor beta stimulus / FCERI mediated Ca+2 mobilization / wound healing / transcription coactivator binding / sequence-specific double-stranded DNA binding / Ca2+ pathway / cellular response to tumor necrosis factor / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / nucleic acid binding / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain ...Nuclear factor of activated T cells (NFAT) / Rel homology domain (RHD), DNA-binding domain / Rel homology domain (RHD), DNA-binding domain / Rel homology dimerisation domain / Rel homology DNA-binding domain / Rel homology dimerisation domain / NF-kappa-B/Rel/dorsal domain profile. / Rel homology domain (RHD), DNA-binding domain superfamily / ig-like, plexins, transcription factors / IPT domain / p53-like transcription factor, DNA-binding / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Nuclear factor of activated T-cells, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsWolfe, S.A. / Zhou, P. / Dotsch, V. / Chen, L. / You, A. / Ho, S.N. / Crabtree, G.R. / Wagner, G. / Verdine, G.L.
CitationJournal: Nature / Year: 1997
Title: Unusual Rel-like architecture in the DNA-binding domain of the transcription factor NFATc.
Authors: Wolfe, S.A. / Zhou, P. / Dotsch, V. / Chen, L. / You, A. / Ho, S.N. / Crabtree, G.R. / Wagner, G. / Verdine, G.L.
History
DepositionJan 18, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HUMAN TRANSCRIPTION FACTOR NFATC1


Theoretical massNumber of molelcules
Total (without water)19,9861
Polymers19,9861
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 40CLOSEST BACKBONE RMSD TO THE MEAN
Representative

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Components

#1: Protein HUMAN TRANSCRIPTION FACTOR NFATC1


Mass: 19985.854 Da / Num. of mol.: 1 / Fragment: DNA-BINDING DOMAIN, RESIDUES 416 - 591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM UNTIL DEPHOSPHORYLATED / Gene: NFATC1 / Plasmid: PLM1 / Gene (production host): NFATC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: O95644

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N NOESY-HSQC
1212D 1H-1H NOESY
1313D 13C NOESY-HSQC
141HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY USING 13C, 15N-LABELED NFATC. IONIC_STRENGTH: 100 MM KCL PRESSURE: NULL SOLVENT SYSTEM: H2O

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX 500BrukerDMX 5005001
Varian UNITY PLUS 750VarianUNITY PLUS 7507502

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
NMR software
NameDeveloperClassification
DIANAWUTHRICHrefinement
DIANAstructure solution
XPLORstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: CALCULATIONS WERE PERFORMED BASED ON 1087 EFFECTIVE NON-HYDROGEN-BOND CONSTRAINTS WITH 3 REDAC CYCLES. STRUCTURES WITH TARGET FUNCTIONS BELOW 10 WERE FURTHER REFINED BY SIMULATED ANNEALING USING X-PLOR.
NMR ensembleConformer selection criteria: CLOSEST BACKBONE RMSD TO THE MEAN
Conformers calculated total number: 40 / Conformers submitted total number: 10

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