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- PDB-2lkx: NMR structure of the homeodomain of Pitx2 in complex with a TAATC... -

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Basic information

Entry
Database: PDB / ID: 2lkx
TitleNMR structure of the homeodomain of Pitx2 in complex with a TAATCC DNA binding site
Components
  • DNA (5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3')
  • Pituitary homeobox 3
KeywordsTRANSCRIPTION/DNA / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


negative regulation of gliogenesis / positive regulation of cell proliferation in midbrain / deltoid tuberosity development / cellular response to glial cell derived neurotrophic factor / prolactin secreting cell differentiation / somatotropin secreting cell differentiation / TFAP2 (AP-2) family regulates transcription of other transcription factors / response to methamphetamine hydrochloride / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / embryonic heart tube left/right pattern formation ...negative regulation of gliogenesis / positive regulation of cell proliferation in midbrain / deltoid tuberosity development / cellular response to glial cell derived neurotrophic factor / prolactin secreting cell differentiation / somatotropin secreting cell differentiation / TFAP2 (AP-2) family regulates transcription of other transcription factors / response to methamphetamine hydrochloride / RNA polymerase II-specific DNA-binding transcription factor binding => GO:0061629 / embryonic heart tube left/right pattern formation / iris morphogenesis / cardiac neural crest cell migration involved in outflow tract morphogenesis / : / lens morphogenesis in camera-type eye / left/right axis specification / chromatin => GO:0000785 / hair cell differentiation / dopaminergic neuron differentiation / response to morphine / camera-type eye development / determination of left/right symmetry / lens development in camera-type eye / odontogenesis / midbrain development / outflow tract morphogenesis / response to immobilization stress / anatomical structure morphogenesis / ribonucleoprotein complex binding / spleen development / response to cocaine / phosphoprotein binding / animal organ morphogenesis / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / 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 / neuronal cell body / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Homeobox protein Pitx/unc30 / OAR domain / OAR motif / OAR domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain ...Homeobox protein Pitx/unc30 / OAR domain / OAR motif / OAR domain profile. / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Pituitary homeobox 3 / Pituitary homeobox 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsclosest to the average, model 1
AuthorsBaird-Titus, J.M. / Doerdelmann, T. / Chaney, B.A. / Clark-Baldwin, K. / Dave, V. / Ma, J.
CitationJournal: Biochemistry / Year: 2005
Title: Solution structure of the K50 class homeodomain PITX2 bound to DNA and implications for mutations that cause Rieger syndrome
Authors: Chaney, B.A. / Clark-Baldwin, K. / Dave, V. / Ma, J. / Rance, M.
History
DepositionOct 21, 2011Deposition site: BMRB / Processing site: RCSB
SupersessionMay 2, 2012ID: 1YZ8
Revision 1.0May 2, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pituitary homeobox 3
B: DNA (5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3')
C: DNA (5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)16,4313
Polymers16,4313
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)17 / 30structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Pituitary homeobox 3 / Homeobox protein PITX3 / Paired-like homeodomain transcription factor 3


Mass: 8486.523 Da / Num. of mol.: 1 / Fragment: Homeobox DNA binding domain residues 62-121
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PITX3, PTX3 / Production host: Escherichia coli (E. coli) / References: UniProt: O75364, UniProt: Q99697*PLUS
#2: DNA chain DNA (5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3')


Mass: 3887.537 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3')


Mass: 4056.646 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1223D 1H-15N NOESY
1312D 1H-13C HSQC aliphatic
1412D 1H-13C HSQC aromatic
1513D CBCA(CO)NH
1613D C(CO)NH
1713D HNCO
1813D HNCA
1913D HN(CA)CB
11013D H(CCO)NH
11113D (H)CCH-TOCSY
11213D 1H-13C NOESY aliphatic
11313D 1H-13C NOESY aromatic
11413D HBHA(CO)NH

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] pitx2 homeodomain, 1 mM DNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3'), 1 mM DNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3'), 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 15N] pitx2 homeodomain, 1 mM DNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3'), 1 mM DNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3'), 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMpitx2 homeodomain-1[U-99% 13C; U-99% 15N]1
1 mMDNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3')-21
1 mMDNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3')-31
1 mMpitx2 homeodomain-4[U-99% 15N]2
1 mMDNA (5'-D(P*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*C)-3')-52
1 mMDNA (5'-D(P*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*G)-3')-62
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AMBERCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollmrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 17

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