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- PDB-2c6y: Crystal structure of interleukin enhancer-binding factor 1 bound ... -

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Basic information

Entry
Database: PDB / ID: 2c6y
TitleCrystal structure of interleukin enhancer-binding factor 1 bound to DNA
Components
  • (INTERLEUKIN 2 PROMOTOR) x 2
  • FORKHEAD BOX PROTEIN K2FOX proteins
KeywordsTRANSCRIPTION REGULATION / DNA-BINDING DOMAIN / FORKHEAD TRANSCRIPTION FACTORS / INTERLEUKIN ENHANCER BINDING FACTOR / WINGED HELIX / FORKHEAD
Function / homology
Function and homology information


canonical glycolysis / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / negative regulation of autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / UCH proteinases / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding ...canonical glycolysis / response to starvation / intracellular glucose homeostasis / regulation of glucose metabolic process / negative regulation of autophagy / DNA-binding transcription repressor activity, RNA polymerase II-specific / UCH proteinases / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / magnesium ion binding / positive regulation of transcription by RNA polymerase II / mitochondrion / nucleoplasm / nucleus
Similarity search - Function
: / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. ...: / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Forkhead box protein K2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsTsai, K.-L. / Huang, C.-Y. / Chang, C.-H. / Sun, Y.-J. / Chuang, W.-J. / Hsiao, C.-D.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Crystal Structure of the Human Foxk1A-DNA Complex and its Implications on the Diverse Binding Specificity of Winged Helix/Forkhead Proteins.
Authors: Tsai, K.-L. / Huang, C.-Y. / Chang, C.-H. / Sun, Y.-J. / Chuang, W.-J. / Hsiao, C.-D.
History
DepositionNov 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORKHEAD BOX PROTEIN K2
B: FORKHEAD BOX PROTEIN K2
C: INTERLEUKIN 2 PROMOTOR
D: INTERLEUKIN 2 PROMOTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4666
Polymers35,4174
Non-polymers492
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.736, 58.736, 324.923
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein FORKHEAD BOX PROTEIN K2 / FOX proteins / INTERLEUKIN ENHANCER-BINDING FACTOR 1 / CELLULAR TRANSCRIPTION FACTOR ILF-1


Mass: 12812.529 Da / Num. of mol.: 2 / Fragment: DNA-BINDING DOMAIN, RESIDUES 251-348
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q01167
#2: DNA chain INTERLEUKIN 2 PROMOTOR


Mass: 4905.229 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 5'-D(*TP*GP*TP*TP*GP*TP*AP*AP*AP*CP*AP*AP* TP*AP*CP*A)-3'
Source: (synth.) HOMO SAPIENS (human)
#3: DNA chain INTERLEUKIN 2 PROMOTOR


Mass: 4887.201 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 5'-D(*AP*TP*GP*TP*AP*TP*TP*GP*TP*TP*TP*AP* CP*AP*AP*C)-3'
Source: (synth.) HOMO SAPIENS (human)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBER BEFORE 1 IS T7 TAG. THE T7 TAGS IN BOTH CHAIN A AND B ARE DISORDERED, AND NOT ...RESIDUE NUMBER BEFORE 1 IS T7 TAG. THE T7 TAGS IN BOTH CHAIN A AND B ARE DISORDERED, AND NOT DETERMINED IN THE MODEL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.4 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1.12714
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2.4→29.44 Å / Num. obs: 12691 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 8.6 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 45.1
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.44 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 577606.57 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: RESIDUE 96-98 IN CHAIN B ARE DISORDERED, AND NOT DETERMINED IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1284 10.1 %RANDOM
Rwork0.233 ---
obs0.233 12691 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 85.5238 Å2 / ksol: 0.430544 e/Å3
Displacement parametersBiso mean: 37.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å212.77 Å20 Å2
2---0.53 Å20 Å2
3---1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1607 650 2 225 2484
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.3
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.521.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it1.692
X-RAY DIFFRACTIONc_scangle_it2.62.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 163 9.8 %
Rwork0.308 1493 -
obs--72.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMDNA-RNA_REP.TOP

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