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- PDB-2nlu: Domain-Swapped Dimer of the PWWP Module of Human Hepatoma-derived... -

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Basic information

Entry
Database: PDB / ID: 2nlu
TitleDomain-Swapped Dimer of the PWWP Module of Human Hepatoma-derived Growth Factor
ComponentsHepatoma-derived growth factor
KeywordsHORMONE/GROWTH FACTOR / HDGF / hHDGF / HRP / HATH / PWWP / Heparin / domain-swapping / 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
Rhinovirus 14, subunit 4 - #150 / : / Rhinovirus 14, subunit 4 / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. / Few Secondary Structures ...Rhinovirus 14, subunit 4 - #150 / : / Rhinovirus 14, subunit 4 / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. / Few Secondary Structures / Irregular / Roll / Mainly Beta
Similarity search - Domain/homology
Hepatoma-derived growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSue, S.C. / Lee, W.T. / Huang, T.H.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: PWWP module of human hepatoma-derived growth factor forms a domain-swapped dimer with much higher affinity for heparin
Authors: Sue, S.C. / Lee, W.T. / Tien, S.C. / Lee, S.C. / Yu, J.G. / Wu, W.J. / Wu, W.G. / Huang, T.H.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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
Revision 1.3Dec 27, 2023Group: 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
B: Hepatoma-derived growth factor


Theoretical massNumber of molelcules
Total (without water)23,1282
Polymers23,1282
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)16 / 100The submitted structures are the 16 structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Hepatoma-derived growth factor / / HDGF / High-mobility group protein 1-like 2 / HMG-1L2


Mass: 11564.120 Da / Num. of mol.: 2 / Fragment: HATH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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
11113C, 15N filtered, 15N edited NOESY-HSQC
12113C, 15N filtered, 13C edited NOESY-HSQC
13213C, 15N filtered, 15N edited NOESY-HSQC
1433D 15N-separated NOESY
1533D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM u-15N, 13C, 2H and unlabeled HATH Dimer; 10mM phosphate buffer, 150mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
21mM u-15N, 2H and u-2H HATH Dimer; 10mM phosphate buffer, 150mM NaCl ;90% H2O, 10% D2O90% H2O/10% D2O
31mM u-15N, 13C HATH Dimer; 10mM phosphate buffer, 150mM NaCl; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 7.4 / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
XwinNMR3.5Brukerprocessing
Sparky3.113T.D.Goddard, D.G.Knellerdata analysis
ARIA1.2M.Nilges, A.M.Gronenborn, G.M.Clorestructure solution
ARIA1.2M.Nilges, A.M.Gronenborn, G.M.Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: The submitted structures are the 16 structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 16

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