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Yorodumi- PDB-5iei: X-ray crystallographic structure of a high affinity IGF2 antagoni... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5iei | ||||||
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Title | X-ray crystallographic structure of a high affinity IGF2 antagonist (Domain11 AB5 RHH) based on human IGF2R domain 11 | ||||||
Components | Cation-independent mannose-6-phosphate receptor | ||||||
Keywords | TRANSPORT PROTEIN / IGF2 / IGF2R / domain 11 | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Nicholls, R.D. / Williams, C. / Strickland, M. / Frago, S. / Hassan, A.B. / Crump, M.P. | ||||||
Funding support | United Kingdom, 1items
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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 | 5iei.cif.gz | 40.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5iei.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 5iei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/5iei ftp://data.pdbj.org/pub/pdb/validation_reports/ie/5iei | HTTPS FTP |
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-Related structure data
Related structure data | 2m68C 2m6tC 1gp0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15554.753 Da / Num. of mol.: 1 / Fragment: UNP residues 1508-1649 / Mutation: Q1569R, P1597H, S1602H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Plasmid: pET26a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11717 | ||
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#2: Chemical | ChemComp-GOL / | ||
#3: Chemical | #4: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.43 % Description: Elongated clear bars, normally crystalise from droplet edge inward. |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2.0 M Ammonium Sulphate, 0.1M Bis-(2-hydroxyethyl)imino-tris(hydroxymethyl methane, pH 7.0. PH range: 6.5-8.0 Temp details: Crystal growth at 277K and 298 led to precipitation or small needles. Optimal growth conditions were at 291K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Jan 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→38.36 Å / Num. obs: 3414 / % possible obs: 99.8 % / Redundancy: 6.2 % / Biso Wilson estimate: 26.5 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.2 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.8→2.86 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 1.35 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GP0 Resolution: 2.8→38.36 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.885 / SU B: 13.074 / SU ML: 0.26 / Cross valid method: THROUGHOUT / ESU R Free: 0.417 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.441 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→38.36 Å
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Refine LS restraints |
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