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Yorodumi- PDB-3gky: The Structural Basis of an ER Stress-Associated Bottleneck in a P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gky | ||||||
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Title | The Structural Basis of an ER Stress-Associated Bottleneck in a Protein Folding Landscape | ||||||
Components |
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Keywords | HORMONE / protein folding / ER stress-associated / TR transition receptor binding / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Disulfide bond / Glucose metabolism / Pharmaceutical / Secreted | ||||||
Function / homology | Function and homology information Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / lipid biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / positive regulation of protein secretion / hormone activity / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / positive regulation of cell migration / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Liu, M. / Wan, Z.L. / Chu, Y.C. / Alddin, H. / Klaproth, B. / Weiss, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Crystal structure of a "nonfoldable" insulin: IMPAIRED FOLDING EFFICIENCY DESPITE NATIVE ACTIVITY. Authors: Liu, M. / Wan, Z.L. / Chu, Y.C. / Aladdin, H. / Klaproth, B. / Choquette, M. / Hua, Q.X. / Mackin, R.B. / Rao, J.S. / De Meyts, P. / Katsoyannis, P.G. / Arvan, P. / Weiss, M.A. #1: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1988 Title: The structure of 2zn pig insulin crystal at 1.5 A resolution Authors: Baker, E.N. / Blujdell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D. / Isaacs, N.W. / Reynolds, C.D. #2: Journal: Nature / Year: 1976 Title: Structure of insulin in 4-zinc insulin Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D. #3: Journal: Nature / Year: 1989 Title: Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer Authors: Derewenda, U. / Derewenda, Z. / Dodson, E. / Dodson, G. / Reynold, C. / Smith, G. / Sparks, C. / Swenson, D. #4: Journal: J.Biol.Chem. / Year: 2006 Title: Toward the active conformation of insulin: stereospecific modulation of a structural swith in the B chain Authors: Hua, Q.X. / Nakagawa, S. / Hu, S.Q. / Jia, W. / Wang, S. / Weiss, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gky.cif.gz | 36.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gky.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gky_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 3gky_full_validation.pdf.gz | 454.8 KB | Display | |
Data in XML | 3gky_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 3gky_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/3gky ftp://data.pdbj.org/pub/pdb/validation_reports/gk/3gky | HTTPS FTP |
-Related structure data
Related structure data | 1trzS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2406.714 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: biosynthetic sequence / Source: (synth.) Sus scrofa (pig) / References: UniProt: P01315 #2: Protein/peptide | Mass: 3403.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: biosynthetic sequence / Source: (synth.) Sus scrofa (pig) / References: UniProt: P01315 |
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-Non-polymers , 4 types, 130 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IPH / | #6: Water | ChemComp-HOH / | |
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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: 1.85 Å3/Da / Density % sol: 33.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 0.02 M Tris, 0.05 M sodium citrate, 5% acetone, 0.03% phenol, 0.01% zinc acetate, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.948 Å |
Detector | Detector: CCD / Date: Feb 11, 2004 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.948 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→22.58 Å / Num. all: 7752 / Num. obs: 7299 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 390252.65 / Redundancy: 6.4 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 3 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 7.4 / Num. unique all: 1027 / % possible all: 90.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1TRZ Resolution: 1.8→22.58 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 39.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→22.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022
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