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Yorodumi- PDB-1rmj: C-terminal domain of insulin-like growth factor (IGF) binding pro... -
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-Basic information
Entry | Database: PDB / ID: 1rmj | ||||||
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Title | C-terminal domain of insulin-like growth factor (IGF) binding protein-6: structure and interaction with IGF-II | ||||||
Components | Insulin-like growth factor binding protein 6 | ||||||
Keywords | HORMONE/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 / negative regulation of cell population proliferation / signaling receptor binding / signal transduction / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / distance geometry simulated annealing | ||||||
Authors | Headey, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rmj.cif.gz | 631.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rmj.ent.gz | 546.4 KB | Display | PDB format |
PDBx/mmJSON format | 1rmj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rmj_validation.pdf.gz | 362.6 KB | Display | wwPDB validaton report |
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Full document | 1rmj_full_validation.pdf.gz | 525.6 KB | Display | |
Data in XML | 1rmj_validation.xml.gz | 44.9 KB | Display | |
Data in CIF | 1rmj_validation.cif.gz | 72.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/1rmj ftp://data.pdbj.org/pub/pdb/validation_reports/rm/1rmj | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | 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 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 3D heteronuclear techniques. |
-Sample preparation
Details | Contents: 1 mM protein 10 mM sodium acetate 0.02 % sodium azide Solvent system: 95% H2O/5% D2O |
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Sample conditions | Ionic strength: 10 mM sodium acetate / pH: 4.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | ||||||||||||||||||||
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Radiation wavelength | Relative weight: 1 | ||||||||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: 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 representative | Selection criteria: closest to the average | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 |