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- PDB-2l7m: Solution Structure of the Pitx2 Homeodomain R24H mutant -

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Basic information

Entry
Database: PDB / ID: 2l7m
TitleSolution Structure of the Pitx2 Homeodomain R24H mutant
ComponentsPituitary homeobox 2
KeywordsTRANSCRIPTION / Homeodomain / DNA-binding
Function / homology
Function and homology information


deltoid tuberosity development / prolactin secreting cell differentiation / somatotropin secreting cell differentiation / TFAP2 (AP-2) family regulates transcription of other transcription factors / embryonic heart tube left/right pattern formation / iris morphogenesis / cardiac neural crest cell migration involved in outflow tract morphogenesis / left/right axis specification / hair cell differentiation / camera-type eye development ...deltoid tuberosity development / prolactin secreting cell differentiation / somatotropin secreting cell differentiation / TFAP2 (AP-2) family regulates transcription of other transcription factors / embryonic heart tube left/right pattern formation / iris morphogenesis / cardiac neural crest cell migration involved in outflow tract morphogenesis / left/right axis specification / hair cell differentiation / camera-type eye development / determination of left/right symmetry / odontogenesis / outflow tract morphogenesis / anatomical structure morphogenesis / ribonucleoprotein complex binding / spleen development / phosphoprotein binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor 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 / positive regulation of cell population proliferation / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / 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
Pituitary homeobox 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
Model detailsminimized average, model 20
AuthorsDoerdelmann, T. / Rance, M. / Kojetin, D.J. / Baird-Titus, J.M.
CitationJournal: To be Published
Title: Solution Structure of the Pitx2 Homeodomain R24H mutant
Authors: Doerdelmann, T. / Kojetin, D.J. / Baird-Titus, J.M. / Rance, M.
History
DepositionDec 14, 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)8,4671
Polymers8,4671
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)20 / 20structures with the lowest 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: 8467.477 Da / Num. of mol.: 1 / Fragment: Homeobox domain residues 85-144 / Mutation: R24H
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) / 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
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCA
1613D HN(CA)CB
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1913D (H)CCH-TOCSY
11013D H(CCO)NH

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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 R24H, 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 R24H-4[U-98% 13C; U-98% 15N]1
Sample conditionsIonic strength: 0.15 / 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
Amber11Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRViewJohnson, One Moon Scientificchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1467 / NOE intraresidue total count: 402 / NOE long range total count: 269 / NOE medium range total count: 420 / NOE sequential total count: 376
NMR representativeSelection criteria: minimized average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.156 Å

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