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- PDB-1rmj: C-terminal domain of insulin-like growth factor (IGF) binding pro... -

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Basic information

Entry
Database: PDB / ID: 1rmj
TitleC-terminal domain of insulin-like growth factor (IGF) binding protein-6: structure and interaction with IGF-II
ComponentsInsulin-like growth factor binding protein 6
KeywordsHORMONE/GROWTH FACTOR / Insulin-like growth factor binding protein / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


insulin-like growth factor binary complex / regulation of insulin-like growth factor receptor signaling pathway / positive regulation of stress-activated MAPK cascade / insulin-like growth factor II binding / insulin-like growth factor I binding / fibronectin binding / negative regulation of canonical Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell migration / positive regulation of MAPK cascade ...insulin-like growth factor binary complex / regulation of insulin-like growth factor receptor signaling pathway / positive regulation of stress-activated MAPK cascade / insulin-like growth factor II binding / insulin-like growth factor I binding / fibronectin binding / negative regulation of canonical Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell migration / positive regulation of MAPK cascade / signaling receptor binding / negative regulation of cell population proliferation / signal transduction / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin-like growth factor-binding protein 6 / Thyroglobulin type-1 / Invariant Chain; Chain I / Insulin-like growth factor-binding protein family 1-6, chordata / 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 ...Insulin-like growth factor-binding protein 6 / Thyroglobulin type-1 / Invariant Chain; Chain I / Insulin-like growth factor-binding protein family 1-6, chordata / 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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsHeadey, S.J. / Keizer, D.W. / Yao, S. / Brasier, G. / Kantharidis, P. / Bach, L.A. / Norton, R.S.
Citation
Journal: Mol.Endocrinol. / Year: 2004
Title: C-terminal domain of insulin-like growth factor (IGF) binding protein-6: structure and interaction with IGF-II.
Authors: Headey, S.J. / Keizer, D.W. / Yao, S. / Brasier, G. / Kantharidis, P. / Bach, L.A. / Norton, R.S.
#1: Journal: J.Biomol.NMR / Year: 2003
Title: 1H, 13C and 15N resonance assignments of the C-terminal domain of insulin-like growth factor binding protein-6 (IGFBP-6).
Authors: Headey, S.J. / Yao, S. / Parker, N.J. / Kantharidis, P. / Bach, L.A. / Norton, R.S.
#2: Journal: Febs Lett. / Year: 2004
Title: Binding site for the C-domain of insulin-like growth factor (IGF) binding protein-6 on IGF-II; implications for inhibition of IGF actions.
Authors: Headey, S.J. / Keizer, D.W. / Yao, S. / Wallace, J.C. / Bach, L.A. / Norton, R.S.
#3: Journal: Biochemistry / Year: 2004
Title: C-Terminal Domain of Insulin-like Growth Factor (IGF) Binding Protein 6: Conformational Exchange and Its Correlation with IGF-II Binding
Authors: Yao, S. / Headey, S.J. / Keizer, D.W. / Bach, L.A. / Norton, R.S.
History
DepositionNov 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 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_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 / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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:
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Assembly

Deposited unit
A: Insulin-like growth factor binding protein 6


Theoretical massNumber of molelcules
Total (without water)12,0761
Polymers12,0761
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 / 50structures with the lowest energy
RepresentativeModel #20closest to the average

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Components

#1: Protein Insulin-like growth factor binding protein 6 / IGFBP-6 / IBP-6 / IGF-binding protein 6


Mass: 12076.315 Da / Num. of mol.: 1
Fragment: C-terminal Domain, sequence database resiude 161-240
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGFBP6, IBP6 / Plasmid: pProEX HTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P24592
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
1213D 13C-separated NOESY
131HNHA
NMR detailsText: This structure was determined using standard 3D heteronuclear techniques.

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Sample preparation

DetailsContents: 1 mM protein 10 mM sodium acetate 0.02 % sodium azide
Solvent system: 95% H2O/5% D2O
Sample conditionsIonic strength: 10 mM sodium acetate / pH: 4.5 / 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 AMXBrukerAMX5001
Bruker DRXBrukerDRX6002
Bruker8003

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Processing

NMR software
NameVersionClassification
XwinNMR3.5collection
XEASY1.3.13data analysis
CYANA1.0.3refinement
X-PLORstructure solution
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1067 restraints, 912 are NOE-derived distance constraints, 145 dihedral angle restraints,10 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

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