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- PDB-2l7f: Solution Structure of the Pitx2 Homeodomain -

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Basic information

Entry
Database: PDB / ID: 2l7f
TitleSolution Structure of the Pitx2 Homeodomain
ComponentsPituitary homeobox 2
KeywordsTRANSCRIPTION / Pitx2 / Homeodomain / DNA-binding
Function / homology
Function and homology information


subthalamic nucleus development / hypothalamus cell migration / deltoid tuberosity development / pulmonary vein morphogenesis / superior vena cava morphogenesis / cell proliferation involved in outflow tract morphogenesis / left lung morphogenesis / prolactin secreting cell differentiation / somatotropin secreting cell differentiation / pulmonary myocardium development ...subthalamic nucleus development / hypothalamus cell migration / deltoid tuberosity development / pulmonary vein morphogenesis / superior vena cava morphogenesis / cell proliferation involved in outflow tract morphogenesis / left lung morphogenesis / prolactin secreting cell differentiation / somatotropin secreting cell differentiation / pulmonary myocardium development / endodermal digestive tract morphogenesis / TFAP2 (AP-2) family regulates transcription of other transcription factors / extraocular skeletal muscle development / embryonic heart tube left/right pattern formation / iris morphogenesis / vascular associated smooth muscle cell differentiation / atrial cardiac muscle tissue morphogenesis / atrioventricular valve development / embryonic camera-type eye development / ventricular cardiac muscle cell development / cardiac neural crest cell migration involved in outflow tract morphogenesis / left/right axis specification / embryonic digestive tract morphogenesis / hair cell differentiation / camera-type eye development / embryonic hindlimb morphogenesis / determination of left/right symmetry / odontogenesis / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / outflow tract morphogenesis / anatomical structure morphogenesis / ribonucleoprotein complex binding / vasculogenesis / spleen development / regulation of cell migration / phosphoprotein binding / chromatin DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / neuron migration / sequence-specific double-stranded DNA binding / transcription regulator complex / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
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
Pituitary homeobox 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsminimized average, model 7
AuthorsDoerdelmann, T. / Rance, M. / Baird-Titus, J.M. / Kojetin, D.J.
CitationJournal: To be Published
Title: Solution Structure of the Pitx2 Homeodomain
Authors: Doerdelmann, T. / Rance, M. / Baird-Titus, J.M. / Kojetin, D.J.
History
DepositionDec 8, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: Pituitary homeobox 2


Theoretical massNumber of molelcules
Total (without water)8,4871
Polymers8,4871
Non-polymers00
Water00
1


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

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Components

#1: Protein Pituitary homeobox 2 / ALL1-responsive protein ARP1 Homeobox protein PITX2 / Paired-like homeodomain transcription factor ...ALL1-responsive protein ARP1 Homeobox protein PITX2 / Paired-like homeodomain transcription factor 2 / RIEG bicoid-related homeobox transcription factor / Solurshin


Mass: 8486.523 Da / Num. of mol.: 1 / Fragment: Homeobox domain residues 85-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PITX2, ARP1, RGS, RIEG, RIEG1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q99697
Sequence detailsTHE C-TERMINAL 6 AMINO ACIDS (EFIVTD) ARE ADDED FOR PROTEIN STABILITY PURPOSES.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aromatic
1312D 1H-13C HSQC aliphatic
1413D 1H-15N NOESY
1513D 1H-13C NOESY
1613D HN(CA)CB
1713D HNCA
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D HN(COCA)CB

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Sample preparation

DetailsContents: 10 mM sodium phosphate, 150 mM sodium sulphate, 1 mM EDTA, 2 mM [U-98% 13C; U-98% 15N] Pitx2 Homeodomain, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMsodium phosphate-11
150 mMsodium sulphate-21
1 mMEDTA-31
2 mMPitx2 Homeodomain-4[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 150 / pH: 7 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002
Varian INOVAVarianINOVA5003
Varian INOVAVarianINOVA4004

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Zhengrong and Baxprocessing
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 871 / NOE intraresidue total count: 253 / NOE long range total count: 126 / NOE medium range total count: 263 / NOE sequential total count: 229
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: Lowest energy / Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.093 Å
NMR ensemble rmsDistance rms dev: 0 Å / Distance rms dev error: 0 Å

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