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- PDB-1imh: TonEBP/DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1imh
TitleTonEBP/DNA COMPLEX
Components
  • 5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3'
  • 5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3'
  • NUCLEAR FACTOR OF ACTIVATED T CELLS 5
KeywordsTRANSCRIPTION/DNA / BETA BARREL / PROTEIN-DNA COMPLEX / DOUBLE HELIX / DNA ENCIRCLEMENT / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


cytokine production / excretion / regulation of calcineurin-NFAT signaling cascade / calcineurin-NFAT signaling cascade / chromatin => GO:0000785 / positive regulation of leukocyte adhesion to vascular endothelial cell / response to osmotic stress / cellular response to cytokine stimulus / transcription factor binding / positive regulation of non-canonical NF-kappaB signal transduction ...cytokine production / excretion / regulation of calcineurin-NFAT signaling cascade / calcineurin-NFAT signaling cascade / chromatin => GO:0000785 / positive regulation of leukocyte adhesion to vascular endothelial cell / response to osmotic stress / cellular response to cytokine stimulus / transcription factor binding / positive regulation of non-canonical NF-kappaB signal transduction / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Nuclear factor of activated T-cells 5 / 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 ...Nuclear factor of activated T-cells 5 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor of activated T-cells 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.86 Å
AuthorsStroud, J.C. / Lopez-Rodriguez, C. / Rao, A. / Chen, L.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structure of a TonEBP-DNA complex reveals DNA encircled by a transcription factor.
Authors: Stroud, J.C. / Lopez-Rodriguez, C. / Rao, A. / Chen, L.
History
DepositionMay 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-D(*TP*TP*GP*CP*TP*GP*GP*AP*AP*AP*AP*AP*TP*AP*G)-3'
B: 5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3'
C: NUCLEAR FACTOR OF ACTIVATED T CELLS 5
D: NUCLEAR FACTOR OF ACTIVATED T CELLS 5


Theoretical massNumber of molelcules
Total (without water)71,4434
Polymers71,4434
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.568, 95.368, 158.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 4657.059 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid Phase DNA Synthesis
#2: DNA chain 5'-D(*AP*AP*CP*TP*AP*TP*TP*TP*TP*TP*CP*CP*AP*GP*C)-3'


Mass: 4518.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid Phase DNA Synthesis
#3: Protein NUCLEAR FACTOR OF ACTIVATED T CELLS 5 / NF-AT5 / TonEBP


Mass: 31133.607 Da / Num. of mol.: 2 / Fragment: DNA BINDING REGION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NFAT5 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: O94916

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 3000, SODIUM CHLORIDE, MAGNESIUM CHLORIDE, BIS-TRIS PROPANE, SODIUM AZIDE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 300011
2NaClSodium chloride11
3MgCl211
4BIS-TRIS PROPANE11
5SODIUM AZIDE11
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMbis-Tris-BTP-HCl1reservoirpH6.6
2100 mM1reservoirNaCl
33-6 %(w/v)PEG30001reservoir
410 mM1reservoirMgCl2
50.2-0.4 mMprotein1drop
610 mMHEPES1droppH7.5
71 mMdithiothreitol1drop
8100 mM1dropNaCl

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
SYNCHROTRONAPS 14-BM-D20.9622
ROTATING ANODEOTHER31.54
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDSep 12, 2000
RIGAKU RAXIS IV2IMAGE PLATENov 15, 2000Yale Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.96221
31.541
ReflectionResolution: 2.85→30 Å / Num. all: 21763 / Num. obs: 20432 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 39.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.2
Reflection shellResolution: 2.85→2.93 Å / Redundancy: 5 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.77 / Num. unique all: 1757 / Rsym value: 0.676 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS
Starting model: pdb entry 1a02

1a02


Resolution: 2.86→29.5 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 304938.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1358 7.2 %RANDOM
Rwork0.244 ---
obs0.244 18876 87.5 %-
all-20432 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.26 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 69.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.2 Å20 Å20 Å2
2--16.33 Å20 Å2
3----11.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.86→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4368 609 0 0 4977
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 150 6.8 %
Rwork0.363 2054 -
obs--61.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 2 / % reflection Rfree: 7.5 % / Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 69.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.96
LS refinement shell
*PLUS
Rfactor Rfree: 0.392 / % reflection Rfree: 6.8 % / Rfactor Rwork: 0.363 / Rfactor obs: 0.363

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