+Open data
-Basic information
Entry | Database: PDB / ID: 2v5p | |||||||||
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Title | COMPLEX STRUCTURE OF HUMAN IGF2R DOMAINS 11-13 BOUND TO IGF-II | |||||||||
Components |
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Keywords | RECEPTOR/GLYCOPROTEIN / CATION INDEPENDENT MANNOSE 6-PHOSPHATE / MEMBRANE / RECEPTOR / LYSOSOME / TRANSPORT / BETA BARREL / PHOSPHORYLATION / FIBRONECTIN TYPE II / INSULIN-LIKE GROWTH FACTOR / RECEPTOR-GLYCOPROTEIN COMPLEX / POLYMORPHISM / GLYCOPROTEIN / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information spongiotrophoblast cell proliferation / positive regulation of skeletal muscle tissue growth / negative regulation of muscle cell differentiation / Retrograde transport at the Trans-Golgi-Network / embryonic placenta morphogenesis / retromer complex binding / clathrin coat / regulation of muscle cell differentiation / response to tetrachloromethane / insulin-like growth factor receptor activity ...spongiotrophoblast cell proliferation / positive regulation of skeletal muscle tissue growth / negative regulation of muscle cell differentiation / Retrograde transport at the Trans-Golgi-Network / embryonic placenta morphogenesis / retromer complex binding / clathrin coat / regulation of muscle cell differentiation / response to tetrachloromethane / insulin-like growth factor receptor activity / Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R) / IRS-related events triggered by IGF1R / insulin-like growth factor binding / positive regulation by host of viral process / genomic imprinting / positive regulation of organ growth / insulin-like growth factor II binding / trans-Golgi network transport vesicle / exocrine pancreas development / positive regulation of multicellular organism growth / retinoic acid binding / lysosomal transport / positive regulation of vascular endothelial cell proliferation / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / positive regulation of activated T cell proliferation / transmembrane receptor protein tyrosine kinase activator activity / mannose binding / positive regulation of cell division / endocytic vesicle / G-protein alpha-subunit binding / embryonic placenta development / positive regulation of glycogen biosynthetic process / SHC-related events triggered by IGF1R / animal organ regeneration / response to retinoic acid / positive regulation of insulin receptor signaling pathway / transport vesicle / striated muscle cell differentiation / insulin-like growth factor receptor binding / receptor-mediated endocytosis / protein serine/threonine kinase activator activity / post-embryonic development / positive regulation of mitotic nuclear division / insulin-like growth factor receptor signaling pathway / secretory granule membrane / trans-Golgi network membrane / platelet alpha granule lumen / liver development / phosphoprotein binding / clathrin-coated endocytic vesicle membrane / animal organ morphogenesis / growth factor activity / insulin receptor binding / trans-Golgi network / hormone activity / osteoblast differentiation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / glucose metabolic process / positive regulation of peptidyl-tyrosine phosphorylation / late endosome / integrin binding / Cargo recognition for clathrin-mediated endocytosis / Platelet degranulation / signaling receptor activity / insulin receptor signaling pathway / Clathrin-mediated endocytosis / spermatogenesis / in utero embryonic development / positive regulation of MAPK cascade / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / early endosome / endosome membrane / endosome / positive regulation of apoptotic process / G protein-coupled receptor signaling pathway / Golgi membrane / focal adhesion / positive regulation of cell population proliferation / Neutrophil degranulation / regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 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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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v5p.cif.gz | 399.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v5p.ent.gz | 331.3 KB | Display | PDB format |
PDBx/mmJSON format | 2v5p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5p ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5p | HTTPS FTP |
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-Related structure data
Related structure data | 2v5nC 2v5oSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 54414.172 Da / Num. of mol.: 2 / Fragment: DOMAINS 11-13, RESIDUES 1508-1992 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: Protein | Mass: 7484.472 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEM-TEASY / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P01344 #3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / 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. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 68 % |
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Crystal grow | pH: 9 / Details: 0.1 M TRIS-HCL PH 9.0, 15% (V/V) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 13, 2003 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 4.1→20 Å / Num. obs: 14662 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.29 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 4.1→4.2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V5O Resolution: 4.1→47.51 Å / Cor.coef. Fo:Fc: 0.791 / Cor.coef. Fo:Fc free: 0.746 / SU B: 175.868 / SU ML: 1.024 / Cross valid method: THROUGHOUT / ESU R Free: 1.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 90.39 Å2
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Refinement step | Cycle: LAST / Resolution: 4.1→47.51 Å
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Refine LS restraints |
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