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- PDB-2h7t: Solution Structure of the C-terminal Domain of Insulin-like Growt... -

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Basic information

Entry
Database: PDB / ID: 2h7t
TitleSolution Structure of the C-terminal Domain of Insulin-like Growth Factor Binding Protein 2 (IGFBP-2)
ComponentsInsulin-like growth factor-binding protein 2
KeywordsPROTEIN BINDING / Thyroglobulin type 1 fold
Function / homology
Function and homology information


regulation of insulin-like growth factor receptor signaling pathway / insulin-like growth factor II binding / receptor ligand inhibitor activity / insulin-like growth factor I binding / signaling receptor inhibitor activity / protein phosphatase inhibitor activity / positive regulation of activated T cell proliferation / response to retinoic acid / response to mechanical stimulus / cellular response to hormone stimulus ...regulation of insulin-like growth factor receptor signaling pathway / insulin-like growth factor II binding / receptor ligand inhibitor activity / insulin-like growth factor I binding / signaling receptor inhibitor activity / protein phosphatase inhibitor activity / positive regulation of activated T cell proliferation / response to retinoic acid / response to mechanical stimulus / cellular response to hormone stimulus / response to nutrient / response to glucocorticoid / female pregnancy / negative regulation of canonical Wnt signaling pathway / response to estrogen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / osteoblast differentiation / response to estradiol / apical plasma membrane / response to xenobiotic stimulus / signaling receptor binding / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Insulin-like growth factor binding protein 2 / Thyroglobulin type-1 / Invariant Chain; Chain I / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues ...Insulin-like growth factor binding protein 2 / Thyroglobulin type-1 / Invariant Chain; Chain I / Insulin-like growth factor-binding protein family 1-6, chordata / Insulin-like growth factor binding protein, N-terminal, Cys-rich conserved site / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain signature. / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Growth factor receptor cysteine-rich domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Insulin-like growth factor-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKuang, Z.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure, dynamics and heparin binding of the C-terminal domain of insulin-like growth factor-binding protein-2 (IGFBP-2)
Authors: Kuang, Z. / Yao, S. / Keizer, D.W. / Wang, C.C. / Bach, L.A. / Forbes, B.E. / Wallace, J.C. / Norton, R.S.
History
DepositionJun 3, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2007Provider: 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: 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 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-like growth factor-binding protein 2


Theoretical massNumber of molelcules
Total (without water)12,2371
Polymers12,2371
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 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Insulin-like growth factor-binding protein 2 / IGFBP-2 / IBP- 2 / IGF-binding protein 2


Mass: 12236.894 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGFBP2, BP2 / Plasmid: pET32a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18065
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1323D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM C-BP-2 U-15N; 10mM Na acetate, 95% H2O, 5% D2O95% H2O/5% D2O
20.5mM C-BP-2 U-15N, 13C; 10mM Na acetate, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 0.01M / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Bruker Biospincollection
XEASY1.3Bartelsdata analysis
CYANA1.0.3Guentertstructure solution
OPALpKoradirefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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