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- PDB-1ri0: NMR structure of the N-terminal hath domain of human HDGF -

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Basic information

Entry
Database: PDB / ID: 1ri0
TitleNMR structure of the N-terminal hath domain of human HDGF
ComponentsHepatoma-derived growth factor
KeywordsHORMONE/GROWTH FACTOR / HDGF / hath domain / PWWP domain / heparin-binding / growth factor / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


XBP1(S) activates chaperone genes / 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 ...XBP1(S) activates chaperone genes / 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 / actin binding / collagen-containing extracellular matrix / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / RNA binding / extracellular region / 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 speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
AuthorsSue, S.-C. / Chen, J.-Y. / Huang, T.-H.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Solution Structure and Heparin Interaction of Human Hepatoma-derived Growth Factor
Authors: Sue, S.-C. / Chen, J.-Y. / Lee, S.-C. / Wu, W.-G. / Huang, T.-H.
History
DepositionNov 16, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hepatoma-derived growth factor


Theoretical massNumber of molelcules
Total (without water)12,7981
Polymers12,7981
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 / 100target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Hepatoma-derived growth factor / / The hath domain of hHDGF / HDGF / High-mobility group protein 1-like 2 / HMG-1L2


Mass: 12797.549 Da / Num. of mol.: 1 / Fragment: N-terminal 100 residues
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HDGF / Plasmid: pET11d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51858

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined by using standard triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 2 to 3mM 15N and 13C uniform labeled protein, 100mM phosphate buffer, 150mM NaCl, 1mM EDTA
Solvent system: 95% H2O/5% D2O
Sample conditionspH: 6.0 / Pressure: ambient / Temperature: 298 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
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.1Brukerprocessing
AURELIA2.8.13Brukerdata analysis
CYANA1.0.5Peter Guntert, Torsten Herrmannstructure solution
CYANA1.0.5Peter Guntert, Torsten Herrmannrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
Details: The structures are based on a total of 1507 restraints, including 1245 NOE-derived distance constraints, 196 dihedral angle restraints, 66 distance restraints of hydrogen bonds.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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