[English] 日本語
Yorodumi- PDB-1rwe: Enhancing the activity of insulin at receptor edge: crystal struc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rwe | ||||||
---|---|---|---|---|---|---|---|
Title | Enhancing the activity of insulin at receptor edge: crystal structure and photo-cross-linking of A8 analogues | ||||||
Components |
| ||||||
Keywords | HORMONE/GROWTH FACTOR / A8-Histidine human insulin / insulin receptor / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / vasodilation / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / insulin receptor signaling pathway / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protease binding / secretory granule lumen / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Wan, Z. / Xu, B. / Chu, Y.C. / Li, B. / Nakagawa, S.H. / Qu, Y. / Hu, S.Q. / Katsoyannis, P.G. / Weiss, M.A. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Enhancing the activity of insulin at the receptor interface: crystal structure and photo-cross-linking of A8 analogues. Authors: Wan, Z. / Xu, B. / Huang, K. / Chu, Y.C. / Li, B. / Nakagawa, S.H. / Qu, Y. / Hu, S.Q. / Katsoyannis, P.G. / Weiss, M.A. #1: Journal: Biochemistry / Year: 1995 Title: X-ray crystallographic studies on hexameric insulins in the presence of helix-stabilizing agents,thiocyanate, methylparahben, and phenol Authors: Whittingham, J.L. / Chaudhuri, S. / Dodson, E.J. / Moody, P.C. / Dodson, G.G. #2: Journal: Structure / Year: 1995 Title: Role of c-terminal B-chain residues in insulin assemble: the structure of hexameric LysB28ProB29-human insulin Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, D.C. / Smith, G.D. #3: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Phase changes in T3R3f human insulin: temperature or pressure insulin Authors: Smith, G.D. / Blessing, R.H. #4: Journal: J.Mol.Biol. / Year: 2002 Title: Non-standard insulin design:structure-activity relationship at the periphery of the insulin receptor Authors: Weiss, M.A. / Wan, Z.L. / Zhao, M. / Chu, Y.C. / Nakagawa, S.H. / Burke, G.T. / Jia, W.H. / Hellmich, R. / Katsoyannis, P.G. #5: Journal: Biochemistry / Year: 2003 Title: Crystal structure of allo-IleA2-insulin, an , an inactive chiral analogue: implications for the mechanism of receptor binding Authors: Wan, Z.L. / Xu, B. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1rwe.cif.gz | 38.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1rwe.ent.gz | 26 KB | Display | PDB format |
PDBx/mmJSON format | 1rwe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rwe_validation.pdf.gz | 397.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1rwe_full_validation.pdf.gz | 398.2 KB | Display | |
Data in XML | 1rwe_validation.xml.gz | 4 KB | Display | |
Data in CIF | 1rwe_validation.cif.gz | 6.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/1rwe ftp://data.pdbj.org/pub/pdb/validation_reports/rw/1rwe | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
2 |
| |||||||||||||||||||||
3 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||
Details | The biological assembly is hexamer generated from the dimer in the asymmetric unit by the operations: -y,x-y,z and -x+y,-x,z The crystallographic asymmetric unit of insulin consists of two insulin monomers each consisting of two heterochains The entry present coordinates for monomer 1 (chain indicators A and B) and monomer2 (chain indicators C and D) There are two zinc ions per insulin hexamer located on the three-fold axis The conformations of two monomers are different as the result of B change in conformation of first eight residues of the B-chain |
-Components
-Protein/peptide , 2 types, 4 molecules ACBD
#1: Protein/peptide | Mass: 2420.741 Da / Num. of mol.: 2 / Fragment: insulin A chain / Mutation: T8H / Source method: obtained synthetically / Keywords: T8H / References: UniProt: P01308 #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: insulin B chain / Source method: obtained synthetically / References: UniProt: P01308 |
---|
-Non-polymers , 4 types, 141 molecules
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-IPH / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.49 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 6.8 Details: Tris, sodium citrate, acetone, phenol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.80 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.978 |
Detector | Type: ADSC / Detector: CCD / Date: Aug 19, 1998 |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.18 Å / Num. obs: 7426 / % possible obs: 98.4 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23.52 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 9.2 / % possible all: 95.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1TRZ AND 1MPJ Resolution: 1.8→19.18 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH & HUBER
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.1019 Å2 / ksol: 0.336481 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
|