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Open data
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Basic information
Entry | Database: PDB / ID: 1gp3 | ||||||
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Title | Human IGF2R domain 11 | ||||||
![]() | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | ||||||
![]() | RECEPTOR / INSULIN-LIKE GROWTH FACTOR / CATION INDEPENDENT MANNOSE 6-PHOSPHATE / TRANSPORT / BETA BARREL | ||||||
Function / homology | ![]() Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding ...Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / response to tetrachloromethane / insulin-like growth factor receptor activity / insulin-like growth factor binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding / lysosomal transport / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / D-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 / Clathrin-mediated endocytosis / signaling receptor activity / 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brown, J. / Esnouf, R.M. / Jones, M.A. / Linnell, J. / Harlos, K. / Hassan, A.B. / Jones, E.Y. | ||||||
![]() | ![]() Title: Structure of a Functional Igf2R Fragment Determined from the Anomalous Scattering of Sulfur Authors: Brown, J. / Esnouf, R.M. / Jones, M.A. / Linnell, J. / Harlos, K. / Hassan, A.B. / Jones, E.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 40.2 KB | Display | ![]() |
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PDB format | ![]() | 26.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.5 KB | Display | ![]() |
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Full document | ![]() | 427.6 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gp0SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15564.672 Da / Num. of mol.: 1 Fragment: IGF-II BINDING DOMAIN REPEAT 11 RESIDUES 1508-1650 Source method: isolated from a genetically manipulated source Details: RESIDUES VISIBLE IN THE ELECTRON DENSITY MAP CORRESPOND TO MATURE IGF2R RESIDUE NUMBERS 1515 -1647, WITH THE EXCEPTION OF RESIDUES 1618 - 1621 WHERE THE DENSITY IS NOT CONTINUOUS Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
Compound details | TRANSPORT OF PHOSPHORYLATED LYSOSOMAL ENZYMES FROM THE GOLGI COMPLEX AND THE CELL SURFACE TO ...TRANSPORT OF PHOSPHORYL |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE, 0.1 M TRIS HCL PH 8.5, 30 % W/V PEG 4000 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 3 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 2000 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. obs: 9752 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.4 / % possible all: 92.9 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 75027 / Rmerge(I) obs: 0.09 |
Reflection shell | *PLUS % possible obs: 92.9 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1GP0 Resolution: 1.95→29.35 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 397551.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.4069 Å2 / ksol: 0.363344 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→29.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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