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- PDB-1n27: Solution structure of the PWWP domain of mouse Hepatoma-derived g... -

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Basic information

Entry
Database: PDB / ID: 1n27
TitleSolution structure of the PWWP domain of mouse Hepatoma-derived growth factor, related protein 3
ComponentsHepatoma-derived growth factor, related protein 3
KeywordsHORMONE/GROWTH FACTOR / Nuclear translocation / HDGF family / hath / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of microtubule depolymerization / microtubule polymerization / tubulin binding / growth factor activity / neuron projection development / microtubule binding / chromatin remodeling / chromatin binding / nucleoplasm / nucleus ...negative regulation of microtubule depolymerization / microtubule polymerization / tubulin binding / growth factor activity / neuron projection development / microtubule binding / chromatin remodeling / chromatin binding / nucleoplasm / nucleus / cytosol / 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-related protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / torsion angle dynamics, restrained molecular dynamics
AuthorsNameki, N. / Kigawa, T. / Koshiba, S. / Kobayashi, N. / Tochio, N. / Inoue, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Protein Sci. / Year: 2005
Title: Solution structure of the PWWP domain of the hepatoma-derived growth factor family.
Authors: Nameki, N. / Tochio, N. / Koshiba, S. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Fujikura, Y. / Saito, M. / Ikari, M. / Watanabe, M. / Terada, T. / Shirouzu, M. / ...Authors: Nameki, N. / Tochio, N. / Koshiba, S. / Inoue, M. / Yabuki, T. / Aoki, M. / Seki, E. / Matsuda, T. / Fujikura, Y. / Saito, M. / Ikari, M. / Watanabe, M. / Terada, T. / Shirouzu, M. / Yoshida, M. / Hirota, H. / Tanaka, A. / Hayashizaki, Y. / Guntert, P. / Kigawa, T. / Yokoyama, S.
History
DepositionOct 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatoma-derived growth factor, related protein 3


Theoretical massNumber of molelcules
Total (without water)10,6501
Polymers10,6501
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 / 100structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Hepatoma-derived growth factor, related protein 3


Mass: 10649.930 Da / Num. of mol.: 1 / Fragment: PWWP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis system / Gene: 4632410H03 / Plasmid: P020408-01 / References: UniProt: Q9JMG7

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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

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Sample preparation

DetailsContents: 0.7mM PWWP domain U-15N,13C; 20mM phosphate buffer NA; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 6 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.613Kobayashi, N.data analysis
CYANA1.0.6Guentert, P.structure solution
OPALpKoradi, R., Billeter, M., Guentert, P.refinement
RefinementMethod: torsion angle dynamics, restrained molecular dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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