+Open data
-Basic information
Entry | Database: PDB / ID: 2v5n | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF HUMAN IGF2R DOMAINS 11-12 | ||||||
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 / 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 / MAD / Resolution: 3.2 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 |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v5n.cif.gz | 56.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v5n.ent.gz | 42.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5n ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5n | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 32980.461 Da / Num. of mol.: 1 / Fragment: DOMAINS 11 AND 12, RESIDUES 1508-1799 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 | ||
---|---|---|---|
#2: Sugar | 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 PUBMED ID: 2957598. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 Details: 0.2 M POTASSIUM SODIUM TARTRATE, 20% (W/V) PEG 3350, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9789 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 24, 2004 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→45 Å / Num. obs: 6123 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 19.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.5 |
Reflection shell | Resolution: 3.2→3.3 Å / Redundancy: 19.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 4.9 / % possible all: 96.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 3.2→19.73 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.867 / SU B: 64.678 / SU ML: 0.505 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.642 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 97.56 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→19.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|