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- PDB-1a66: SOLUTION NMR STRUCTURE OF THE CORE NFATC1/DNA COMPLEX, 18 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1a66
TitleSOLUTION NMR STRUCTURE OF THE CORE NFATC1/DNA COMPLEX, 18 STRUCTURES
Components
  • CORE NFATC1
  • DNA (5'-D(*CP*AP*AP*TP*TP*TP*TP*CP*CP*TP*CP*G)-3')
  • DNA (5'-D(*CP*GP*AP*GP*GP*AP*AP*AP*AP*TP*TP*G)-3')
KeywordsTRANSCRIPTION/DNA / NFATC1/DNA / REL / NFAT/DNA / ARRE2 / NFAT / NFATC1 / NFATC / NFAT2 / BINARY COMPLEX / TRANSCRIPTION FACTOR / ENHANCEOSOME / IL-2 / COMPLEX / BINARY / TRANSCRIPTION-DNA COMPLEX
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 / protein phosphatase 2B binding / aortic valve morphogenesis / positive regulation of DNA biosynthetic process / CLEC7A (Dectin-1) induces NFAT activation / mitogen-activated protein kinase p38 binding ...skeletal muscle adaptation / negative regulation of vascular associated smooth muscle cell differentiation / mononuclear cell differentiation / calcineurin-NFAT signaling cascade / pulmonary valve morphogenesis / protein phosphatase 2B binding / aortic valve morphogenesis / positive regulation of DNA biosynthetic process / CLEC7A (Dectin-1) induces NFAT activation / mitogen-activated protein kinase p38 binding / response to muscle activity / FK506 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 / cellular response to tumor necrosis factor / Ca2+ pathway / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / 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
DNA / DNA (> 10) / Nuclear factor of activated T-cells, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS, SIMULATED ANNEALING
AuthorsZhou, P. / Sun, L.J. / Doetsch, V. / Wagner, G. / Verdine, G.L.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Solution structure of the core NFATC1/DNA complex.
Authors: Zhou, P. / Sun, L.J. / Dotsch, V. / Wagner, G. / Verdine, G.L.
History
DepositionMar 6, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
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
B: DNA (5'-D(*CP*GP*AP*GP*GP*AP*AP*AP*AP*TP*TP*G)-3')
C: DNA (5'-D(*CP*AP*AP*TP*TP*TP*TP*CP*CP*TP*CP*G)-3')
A: CORE NFATC1


Theoretical massNumber of molelcules
Total (without water)27,3293
Polymers27,3293
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)18 / 18NOE VIOLATION <= 0.4 ANGSTROM, DIHEDRAL ANGLE VIOLATION <= 5 DEGREE
Representative

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Components

#1: DNA chain DNA (5'-D(*CP*GP*AP*GP*GP*AP*AP*AP*AP*TP*TP*G)-3')


Mass: 3735.467 Da / Num. of mol.: 1 / Fragment: 12MER DNA CONTAINING MURINE ARRE2 SITE / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*CP*AP*AP*TP*TP*TP*TP*CP*CP*TP*CP*G)-3')


Mass: 3588.353 Da / Num. of mol.: 1 / Fragment: 12MER DNA CONTAINING MURINE ARRE2 SITE / Source method: obtained synthetically
#3: Protein CORE NFATC1


Mass: 20004.900 Da / Num. of mol.: 1 / Fragment: DNA BINDING DOMAIN OF NFATC1 / Mutation: A1M, L2K, H28R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Gene: NFATC1(416-591) / Plasmid: PLM1-NFATC1(416-591) / Species (production host): Escherichia coli / Gene (production host): NFATC1(416-591) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O95644

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111REF. ZHOU ET AL.
121CELL
1311998
14192(5)
151687-696

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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 DMX500BrukerDMX5005001
Varian VARIAN INOVA 500VarianVARIAN INOVA 5007502
Varian VARIAN UNITY PLUS 750VarianVARIAN UNITY PLUS 7507503

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
DYANA-1.4structure solution
X-PLOR3.1structure solution
RefinementMethod: TORSION ANGLE DYNAMICS, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE FOLLOWING REFERENCE: ZHOU ET AL. (1998). "SOLUTION STRUCTURE OF THE CORE NFATC1/DNA COMPLEX". CELL, 1998, 92(5), 687-696.
NMR ensembleConformer selection criteria: NOE VIOLATION <= 0.4 ANGSTROM, DIHEDRAL ANGLE VIOLATION <= 5 DEGREE / Conformers calculated total number: 18 / Conformers submitted total number: 18

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