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- PDB-2b8a: High Resolution Structure of the HDGF PWWP Domain -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 2b8a
TitleHigh Resolution Structure of the HDGF PWWP Domain
ComponentsHepatoma-derived growth factor
KeywordsHORMONE/GROWTH FACTOR / PWWP / HDGF / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding ...cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding / negative regulation of neuron apoptotic process / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Hepatoma-derived growth factor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsLukasik, S.M. / Cierpicki, T. / Borloz, M. / Grembecka, J. / Everett, A. / Bushweller, J.H.
CitationJournal: Protein Sci. / Year: 2006
Title: High resolution structure of the HDGF PWWP domain: a potential DNA binding domain.
Authors: Lukasik, S.M. / Cierpicki, T. / Borloz, M. / Grembecka, J. / Everett, A. / Bushweller, J.H.
History
DepositionOct 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hepatoma-derived growth factor


Theoretical massNumber of molelcules
Total (without water)12,6431
Polymers12,6431
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)26 / 400
RepresentativeModel #1

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Components

#1: Protein Hepatoma-derived growth factor / HDGF


Mass: 12643.304 Da / Num. of mol.: 1 / Fragment: PWWP Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hdgf / Plasmid: pHIS PARALLEL II / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q8VHK7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131HNHA
242TROSY-HNCO with HN couplings
252TROSY-HNCO with NCo couplings
262TROSY-HNCO with CoCa couplings

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Sample preparation

Details
Solution-IDContentsSolvent system
1HDGF U-15N,13C; 20 mM phosphate buffer 6.5; 50 mM KCl; 1 mM DTT90% H20, 10% D2O
2HDGF U-15N,13C; 20 mM phosphate buffer 6.5; 200 mM NaCl; 1 mM DTT90% H20, 10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
150 mM 6.5 ambient 301 K
2200 mM 6.5 ambient 301 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio et alprocessing
Sparky3.11Goodard and Knellerdata analysis
CNS1.1Brunger et alrefinement
CYANA1.0.5Guntert et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structure is baed on 1415 distance restraints, 79 dihedral angles, 23 hydrogen bonds, 54 JHNHA couplings and 258 RDCs
NMR ensembleConformers calculated total number: 400 / Conformers submitted total number: 26

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