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- PDB-2mh2: Structural insights into the DNA recognition and protein interact... -

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Basic information

Entry
Database: PDB / ID: 2mh2
TitleStructural insights into the DNA recognition and protein interaction domains reveal fundamental homologous DNA pairing properties of HOP2
ComponentsHomologous-pairing protein 2 homolog
KeywordsDNA BINDING PROTEIN / meiosis / homologous recombination / homologous pairing protein
Function / homology
Function and homology information


nuclear glucocorticoid receptor binding / reciprocal meiotic recombination / nuclear thyroid hormone receptor binding / nuclear androgen receptor binding / DNA binding domain binding / nuclear receptor coactivator activity / nuclear estrogen receptor binding / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / DNA binding ...nuclear glucocorticoid receptor binding / reciprocal meiotic recombination / nuclear thyroid hormone receptor binding / nuclear androgen receptor binding / DNA binding domain binding / nuclear receptor coactivator activity / nuclear estrogen receptor binding / protein-containing complex binding / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Homologous-pairing protein 2, winged helix domain / Homologous-pairing protein 2 / Leucine zipper with capping helix domain / TBPIP/Hop2 winged helix domain / Leucine zipper with capping helix domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Homologous-pairing protein 2 homolog
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry
Model detailslowest energy, model1
AuthorsMoktan, H. / Guiraldelli, M.F. / Eyter, C.A. / Zhao, W. / Camerini-Otero, R.D. / Sung, P. / Zhou, D.H. / Pezza, R.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Solution Structure and DNA-binding Properties of the Winged Helix Domain of the Meiotic Recombination HOP2 Protein.
Authors: Moktan, H. / Guiraldelli, M.F. / Eyster, C.A. / Zhao, W. / Lee, C.Y. / Mather, T. / Camerini-Otero, R.D. / Sung, P. / Zhou, D.H. / Pezza, R.J.
History
DepositionNov 13, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homologous-pairing protein 2 homolog


Theoretical massNumber of molelcules
Total (without water)9,2571
Polymers9,2571
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 / 40000back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: Protein Homologous-pairing protein 2 homolog / Hop2 / PSMC3-interacting protein / Proteasome 26S ATPase subunit 3-interacting protein / Tat- ...Hop2 / PSMC3-interacting protein / Proteasome 26S ATPase subunit 3-interacting protein / Tat-binding protein 1-interacting protein / TBP-1-interacting protein


Mass: 9257.393 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-84)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hop2, Psmc3ip, Tbpip / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O35047

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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 HNCO
1613D HNCA
1713D HN(CA)CB
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D 1H-15N TOCSY
11213D HCACO
11313D HN(CO)CA

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Sample preparation

DetailsContents: 6 mg/mL [U-99% 13C; U-99% 15N] Hop2, 5% [U-99% 2H] D2O, 10 mM imidazole, 120 mM sodium chloride, 5% glycerol, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
6 mg/mLHop2-1[U-99% 13C; U-99% 15N]1
5 %D2O-2[U-99% 2H]1
10 mMimidazole-31
120 mMsodium chloride-41
5 %glycerol-51
Sample conditionsIonic strength: 120 / pH: 7.8 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOSCornilescu, Delaglio and Baxdata analysis
CS-ROSETTAShen, Vernon, Baker and Baxstructure solution
RPFHuang, Powers, Montelionerefinement
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonstructure validation
RefinementMethod: distance geometry / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 78 / Protein psi angle constraints total count: 78
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 40000 / Conformers submitted total number: 20

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