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- PDB-2k27: Solution structure of Human Pax8 Paired Box Domain -

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Basic information

Entry
Database: PDB / ID: 2k27
TitleSolution structure of Human Pax8 Paired Box Domain
ComponentsPaired box protein Pax-8
KeywordsTRANSCRIPTION REGULATOR / Paired Domain / Pax8 / solution structure / triple frequency / 3D NMR / induced fit / Alternative splicing / Developmental protein / Differentiation / Disease mutation / DNA-binding / Nucleus / Paired box / Phosphoprotein / Polymorphism / Transcription / Transcription regulation
Function / homology
Function and homology information


pronephric field specification / metanephric comma-shaped body morphogenesis / negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis / negative regulation of apoptotic process involved in metanephric collecting duct development / negative regulation of apoptotic process involved in metanephric nephron tubule development / positive regulation of metanephric DCT cell differentiation / regulation of thyroid-stimulating hormone secretion / metanephric nephron tubule formation / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development ...pronephric field specification / metanephric comma-shaped body morphogenesis / negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis / negative regulation of apoptotic process involved in metanephric collecting duct development / negative regulation of apoptotic process involved in metanephric nephron tubule development / positive regulation of metanephric DCT cell differentiation / regulation of thyroid-stimulating hormone secretion / metanephric nephron tubule formation / negative regulation of mesenchymal cell apoptotic process involved in metanephros development / pronephros development / mesenchymal to epithelial transition involved in metanephros morphogenesis / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / thyroid-stimulating hormone receptor activity / positive regulation of thyroid hormone generation / otic vesicle development / metanephric distal convoluted tubule development / metanephric epithelium development / Formation of intermediate mesoderm / urogenital system development / regulation of metanephric nephron tubule epithelial cell differentiation / cellular response to gonadotropin stimulus / metanephric S-shaped body morphogenesis / sulfur compound metabolic process / mesonephros development / sensory organ development / Formation of the nephric duct / positive regulation of branching involved in ureteric bud morphogenesis / ventricular septum development / negative regulation of cardiac muscle cell apoptotic process / inner ear morphogenesis / branching involved in ureteric bud morphogenesis / thyroid gland development / anatomical structure morphogenesis / central nervous system development / kidney development / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / regulation of apoptotic process / 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 / DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Paired-box protein 2 C-terminal / Paired-box protein 2 C terminal / Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...Paired-box protein 2 C-terminal / Paired-box protein 2 C terminal / Paired domain / Paired DNA-binding domain / PAX family / 'Paired box' domain / Paired DNA-binding domain signature. / Paired DNA-binding domain profile. / Paired Box domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Paired box protein Pax-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular mechanics
Model detailsPax8 Paired Box Domain unveiled by means of 3D NMR techniques.
AuthorsCodutti, L. / Esposito, G. / Corazza, A. / Fogolari, F. / Tell, G. / Vascotto, C. / van Ingen, H. / Boelens, R. / Viglino, P. / Quadrifoglio, F.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Solution Structure of DNA-free Pax-8 Paired Box Domain Accounts for Redox Regulation of Transcriptional Activity in the Pax Protein Family.
Authors: Codutti, L. / van Ingen, H. / Vascotto, C. / Fogolari, F. / Corazza, A. / Tell, G. / Quadrifoglio, F. / Viglino, P. / Boelens, R. / Esposito, G.
History
DepositionMar 26, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Paired box protein Pax-8


Theoretical massNumber of molelcules
Total (without water)17,4481
Polymers17,4481
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Paired box protein Pax-8


Mass: 17447.936 Da / Num. of mol.: 1 / Fragment: Pax8 Paired Box Domain (UNP residues 1-143)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAX8 / Plasmid: pLysS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q06710

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Pax8 Paired Box Domain unveiled by means of 3D NMR techniques.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC CT
1313D CBCA(CO)NH
1413D C(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CA)CB
1813D HN(CO)CA
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11213D CBCANH
11313D HN(COCA)CB

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Sample preparation

DetailsContents: 0.9 mM [U-100% 13C; U-100% 15N] Pax8 Paired Box Domain, 40 uM DSS, 50 mM sodium phosphate, 0.1 % sodium azide, 15 mM [U-100% 2H] DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMPax8 Paired Box Domain[U-100% 13C; U-100% 15N]1
40 uMDSS1
50 mMsodium phosphate1
0.1 %sodium azide1
15 mMDTT[U-100% 2H]1
Sample conditionsIonic strength: 50 / pH: 6.2 / Pressure: ambient / Temperature: 298.00 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker Avance 2BrukerAvance 27502

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
TALOS(NMR-Pipe 3.5)Cornilescu, Delaglio and Baxdata analysis
ProcheckNMR3.4Laskowski and MacArthurvalidation
TopSpin1.3Bruker Biospincollection
TopSpin1.3Bruker Biospinprocessing
CARA1.8.4Rochus Kellerchemical shift assignment
CARA1.8.4Rochus Kellerdata analysis
CARA1.8.4Rochus Kellerpeak picking
Discover2.98Accelrys Software Inc.refinement
AQUA3.2Rullmann, Doreleijers and Kapteinvalidation
WHAT IFVriendvalidation
RefinementMethod: molecular mechanics / Software ordinal: 1
Details: Minimization was performed by means of Discover, with 200 iterations using the steep descent and 800 iterations using the conjugate gradients algorithms. c-terminal superposition is ...Details: Minimization was performed by means of Discover, with 200 iterations using the steep descent and 800 iterations using the conjugate gradients algorithms. c-terminal superposition is performed between residues 87-135 and the n-terminal superposition can be performed between 29-62.
NMR constraintsNOE constraints total: 1794 / NOE intraresidue total count: 946 / NOE long range total count: 75 / NOE medium range total count: 185 / NOE sequential total count: 588 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 61 / Protein psi angle constraints total count: 62
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 300 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: -0.57 Å / Maximum upper distance constraint violation: 2.82 Å

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