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Yorodumi- PDB-2m68: NMR solution structure ensemble of 3-4D mutant domain 11 IGF2R in... -
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-Basic information
Entry | Database: PDB / ID: 2m68 | ||||||
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Title | NMR solution structure ensemble of 3-4D mutant domain 11 IGF2R in complex with IGF2 (domain 11 structure only) | ||||||
Components | Insulin-like growth factor 2 receptor variant | ||||||
Keywords | ANTITUMOR PROTEIN / antitumor / directed evolution / high affinity | ||||||
Function / homology | Function and homology information Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / retromer complex binding / clathrin coat / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / positive regulation by host of viral process / insulin-like growth factor II binding / trans-Golgi network transport vesicle / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / mannose binding / endocytic vesicle / G-protein alpha-subunit binding / animal organ regeneration / response to retinoic acid / transport vesicle / receptor-mediated endocytosis / post-embryonic development / secretory granule membrane / trans-Golgi network membrane / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / late endosome / Cargo recognition for clathrin-mediated endocytosis / signaling receptor activity / Clathrin-mediated endocytosis / spermatogenesis / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / extracellular exosome / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
Model details | fewest violations, model1 | ||||||
Authors | Strickland, M. / Williams, C. / Richards, E. / Minnall, L. / Crump, M.P. / Frago, S. / Hughes, J. / Garner, L. / Hoppe, H. / Rezgui, D. ...Strickland, M. / Williams, C. / Richards, E. / Minnall, L. / Crump, M.P. / Frago, S. / Hughes, J. / Garner, L. / Hoppe, H. / Rezgui, D. / Zaccheo, O.J. / Prince, S.N. / Hassan, A.B. / Whittaker, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Functional evolution of IGF2:IGF2R domain 11 binding generates novel structural interactions and a specific IGF2 antagonist. Authors: Frago, S. / Nicholls, R.D. / Strickland, M. / Hughes, J. / Williams, C. / Garner, L. / Surakhy, M. / Maclean, R. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Ebner, D. / Sanegre, S. / Yu, S. ...Authors: Frago, S. / Nicholls, R.D. / Strickland, M. / Hughes, J. / Williams, C. / Garner, L. / Surakhy, M. / Maclean, R. / Rezgui, D. / Prince, S.N. / Zaccheo, O.J. / Ebner, D. / Sanegre, S. / Yu, S. / Buffa, F.M. / Crump, M.P. / Hassan, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m68.cif.gz | 826.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2m68.ent.gz | 691.1 KB | Display | PDB format |
PDBx/mmJSON format | 2m68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/2m68 ftp://data.pdbj.org/pub/pdb/validation_reports/m6/2m68 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15433.587 Da / Num. of mol.: 1 / Fragment: Domain 11 / Mutation: Q1571L ,S1466A, G1467K, K1468G, G1469W, L1470G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Domain 11 IGF2R / Production host: Escherichia coli (E. coli) / References: UniProt: Q59EZ3, UniProt: P11717*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Ensemble of 20 structures of the 3-4D mutant of domain 11 IGF2R in complex with IGF2. The structure concerns the domain 11 portion only. The mutant hosts 5 mutations in the AB loop in ...Details: Ensemble of 20 structures of the 3-4D mutant of domain 11 IGF2R in complex with IGF2. The structure concerns the domain 11 portion only. The mutant hosts 5 mutations in the AB loop in comparison to human domain 11 IGF2R. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
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Sample conditions |
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-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 3176 / NOE intraresidue total count: 1242 / NOE long range total count: 776 / Hydrogen bond constraints total count: 52 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: fewest violations | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0 ° Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.1 Å / Maximum torsion angle constraint violation: 5 ° / Maximum upper distance constraint violation: 0.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0066 Å / Distance rms dev error: 0.0003 Å |