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- PDB-2lt7: Solution NMR structure of Kaiso zinc finger DNA binding domain in... -

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Basic information

Entry
Database: PDB / ID: 2lt7
TitleSolution NMR structure of Kaiso zinc finger DNA binding domain in complex with Kaiso binding site DNA
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
  • Transcriptional regulator Kaiso
KeywordsMETAL BINDING PROTEIN/DNA / zinc finger / double helix / METAL BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / Double Stranded RNA Binding Domain / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily ...Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / Double Stranded RNA Binding Domain / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsBuck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H. / Wilson, I.A. / Wright, P.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso.
Authors: Buck-Koehntop, B.A. / Stanfield, R.L. / Ekiert, D.C. / Martinez-Yamout, M.A. / Dyson, H.J. / Wilson, I.A. / Wright, P.E.
History
DepositionMay 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator Kaiso
D: DNA (5'-D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9336
Polymers27,7373
Non-polymers1963
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcriptional regulator Kaiso / Zinc finger and BTB domain-containing protein 33


Mass: 16086.575 Da / Num. of mol.: 1 / Fragment: zinc finger DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB33, KAISO, ZNF348 / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)[DNAY] / References: UniProt: Q86T24
#2: DNA chain DNA (5'-D(*GP*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')


Mass: 5780.749 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*AP*C)-3')


Mass: 5869.810 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D HNCO
1423D HNCA
1523D HN(CA)CB
1623D CBCA(CO)NH
1723D HN(CO)CA
1833D (H)CCH-COSY
1933D CBCGCD
11013D 1H-15N NOESY
11133D 1H-13C NOESY
11222D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
1500 uM [U-13C; U-15N] Kaiso, 500 uM Kaiso binding sequence (KBS), 10 mM Tris, 1 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
2500 uM [U-100% 13C; U-100% 15N; U-80% 2H] Kaiso, 500 uM Kaiso binding sequence (KBS), 10 mM Tris, 1 mM TCEP, 95% H2O/5% D2O95% H2O/5% D2O
3500 uM [U-13C; U-15N] Kaiso, 500 uM Kaiso binding sequence (KBS), 10 mM Tris, 1 mM TCEP, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 uMKaiso-1[U-13C; U-15N]1
500 uMKaiso binding sequence (KBS)-21
10 mMTris-31
1 mMTCEP-41
500 uMKaiso-5[U-100% 13C; U-100% 15N; U-80% 2H]2
500 uMKaiso binding sequence (KBS)-62
10 mMTris-72
1 mMTCEP-82
500 uMKaiso-9[U-13C; U-15N]3
500 uMKaiso binding sequence (KBS)-103
10 mMTris-113
1 mMTCEP-123
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker DMXBrukerDMX8003
Bruker DMXBrukerDMX9004
Bruker DRXBrukerDRX7505

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Processing

NMR software
NameDeveloperClassification
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
CYANAGuntert, Mumenthaler and Wuthrichpeak picking
NMRViewJohnson, One Moon Scientificdata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxchemical shift calculation
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1347 / NOE intraresidue total count: 195 / NOE long range total count: 499 / NOE medium range total count: 258 / NOE sequential total count: 395 / Protein phi angle constraints total count: 131 / Protein psi angle constraints total count: 131
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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