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Yorodumi- PDB-2l2a: Mutated Domain 11 of the Cytoplasmic region of the Cation-indepen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2l2a | ||||||
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Title | Mutated Domain 11 of the Cytoplasmic region of the Cation-independent mannose-6-phosphate receptor | ||||||
Components | Insulin-like growth factor 2 receptor variant | ||||||
Keywords | TRANSPORT PROTEIN / mannose 6 phosphate receptor / protein evolution / Insulin-like growth factor 2 / Genomic imprinting | ||||||
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 / simulated annealing, simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Williams, C. / Hoppe, H. / Rezgui, D. / Strickland, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. ...Williams, C. / Hoppe, H. / Rezgui, D. / Strickland, M. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Forbes, B. / Jones, E.Y. / Crump, M.P. / Hassan, A.B. | ||||||
Citation | Journal: Science / Year: 2012 Title: An exon splice enhancer primes IGF2:IGF2R binding site structure and function evolution. Authors: Williams, C. / Hoppe, H.J. / Rezgui, D. / Strickland, M. / Forbes, B.E. / Grutzner, F. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Nolan, C.M. / Mungall, A. ...Authors: Williams, C. / Hoppe, H.J. / Rezgui, D. / Strickland, M. / Forbes, B.E. / Grutzner, F. / Frago, S. / Ellis, R.Z. / Wattana-Amorn, P. / Prince, S.N. / Zaccheo, O.J. / Nolan, C.M. / Mungall, A.J. / Jones, E.Y. / 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 | 2l2a.cif.gz | 910.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l2a.ent.gz | 802.2 KB | Display | PDB format |
PDBx/mmJSON format | 2l2a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/2l2a ftp://data.pdbj.org/pub/pdb/validation_reports/l2/2l2a | HTTPS FTP |
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-Related structure data
Related structure data | 2l29C 2l2gC 2llaC C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15434.524 Da / Num. of mol.: 1 / Fragment: domain 11, residues 1431-1570 / Mutation: E1544K, K1545S, L1547V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: igf2r / Plasmid: pET26a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q59EZ3, UniProt: P11717*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: E4 IGF2R domain 11 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 5% D2O, 10 mM [U-99% 2H] sodium acetate, 0.5-1 mM [U-98% 13C; U-98% 15N] IGF2R, 100 uM EDTA, 95% H2O/5% D2O Solvent system: 95% H2O/5% D2O | ||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 4.2 / Pressure: ambient / Temperature: 310 K |
-NMR measurement
NMR spectrometer | Type: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, simulated annealing / Software ordinal: 1 Details: ARIA2.2 protocol. Cool_1 and cool_2 steps increased to 40K and cool_2, ARIA2.2 water refinement modified with RECOORD water refinement parameters | ||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |