+Open data
-Basic information
Entry | Database: PDB / ID: 2v5o | ||||||
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Title | STRUCTURE OF HUMAN IGF2R DOMAINS 11-14 | ||||||
Components | CATION-INDEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR | ||||||
Keywords | RECEPTOR / CATION INDEPENDENT MANNOSE 6-PHOSPHATE / MEMBRANE / LYSOSOME / TRANSPORT / BETA BARREL / PHOSPHORYLATION / FIBRONECTIN TYPE II / INSULIN-LIKE GROWTH FACTOR / GLYCOPROTEIN / TRANSMEMBRANE | ||||||
Function / homology | Function and homology information 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 / Cargo recognition for clathrin-mediated endocytosis / late endosome / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Brown, J. / Delaine, C. / Zaccheo, O.J. / Siebold, C. / Gilbert, R.J. / van Boxel, G. / Denley, A. / Wallace, J.C. / Hassan, A.B. / Forbes, B.E. / Jones, E.Y. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Structure and Functional Analysis of the Igf-II/Igf2R Interaction Authors: Brown, J. / Delaine, C. / Zaccheo, O.J. / Siebold, C. / Gilbert, R.J. / Van Boxel, G. / Denley, A. / Wallace, J.C. / Hassan, A.B. / Forbes, B.E. / Jones, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v5o.cif.gz | 117.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v5o.ent.gz | 87.5 KB | Display | PDB format |
PDBx/mmJSON format | 2v5o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5o ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5o | HTTPS FTP |
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-Related structure data
Related structure data | 2v5nSC 2v5pC 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: 69334.406 Da / Num. of mol.: 1 / Fragment: DOMAINS 11-14, RESIDUES 1508-2128 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Organ: PLACENTA / Plasmid: PEE14 / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster) / Variant (production host): LECR 3.2.8.1 / References: UniProt: P11717 | ||||
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#2: Sugar | #3: Chemical | Sequence details | THE CONFLICT INDICATED IN THE SEQADV RECORDS BELOW HAS BEEN DESCRIBED IN UNIPROT ENTRY P11717 UNDER ...THE CONFLICT INDICATED IN THE SEQADV RECORDS BELOW HAS BEEN DESCRIBED IN UNIPROT ENTRY P11717 UNDER REFERENCE WITH PUBMEDID: 2957598. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 63 % |
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Crystal grow | pH: 6.4 / Details: 0.1 M MES PH6.4, 2.5% (W/V) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 15, 2004 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→30 Å / Num. obs: 19919 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 92.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V5N Resolution: 2.91→28.46 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.837 / SU B: 56.509 / SU ML: 0.465 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.749 / ESU R Free: 0.449 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 65.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.91→28.46 Å
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Refine LS restraints |
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