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Yorodumi- PDB-1q4v: CRYSTAL STRUCTURE OF ALLO-ILEA2-INSULIN, AN INACTIVE CHIRAL ANALO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q4v | |||||||||
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Title | CRYSTAL STRUCTURE OF ALLO-ILEA2-INSULIN, AN INACTIVE CHIRAL ANALOGUE: IMPLICATIONS FOR THE MECHANISM OF RECEPTOR | |||||||||
Components | (Insulin) x 2 | |||||||||
Keywords | HORMONE/GROWTH FACTOR / allo-Ile-A2-insulin / protein unfolding / 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 / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Wan, Z.L. / Xu, B. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A. | |||||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal structure of allo-Ile(A2)-insulin, 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. #1: Journal: J.Mol.Biol. / Year: 2002 Title: CHIRAL MUTAGENESIS OF INSULIN'S HIDDEN RECEPTOR-BINDING SURFACE: STRUCTURE OF AN ALLO-ISOLEUCINE (A2) ANALOGUE Authors: Xu, B. / Hua, Q.X. / NAKAGAWA, S.H. / JIA, W. / CHU, Y.C. / KASOYANNIS, P.G. / WEISS, M.A. #2: Journal: Protein Sci. / Year: 2002 Title: A CAVITY-FORMING MUTATION IN INSULIN INDUCES SEGMENTAL UNFOLDING OF A SURROUNDING ALPHA-HELIX Authors: XU, B. / HUA, Q.X. / NAKAGAWA, S.H. / JIA, W. / CHU, Y.C. / KATSOYANNIS, P.G. / WEISS, M.A. #3: Journal: J.Mol.Biol. / Year: 2002 Title: NON-STANDARD INSULIN DESIGN: STRUCTURE-ACTIVITY RELATIONSHIPS AT THE PERIPHERY OF THE INSULIN Receptor Authors: WEISS, M.A. / WAN, Z. / ZHAO, M. / CHU, Y.C. / NAKAGAWA, S.H. / BURKE, G.T. / JIA, W. / HELLMICH, R. / KATSOYANNIS, P.G. #4: Journal: Trends Biochem.Sci. / Year: 1999 Title: IS PROTEIN FOLDING HIERARCHIC? I. LOCAL STRUCTURE AND PEPTIDE FOLDING Authors: BALDWIN, R.L. / ROSE, G.D. #5: Journal: Trends Biochem.Sci. / Year: 1999 Title: IS PROTEIN FOLDING HIERARCHIC? II. FOLDING INTERMEDIATES AND TRANSITION STATES Authors: BALDWIN, R.L. / ROSE, G.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q4v.cif.gz | 36 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q4v.ent.gz | 24.5 KB | Display | PDB format |
PDBx/mmJSON format | 1q4v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1q4v_validation.pdf.gz | 397.8 KB | Display | wwPDB validaton report |
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Full document | 1q4v_full_validation.pdf.gz | 398 KB | Display | |
Data in XML | 1q4v_validation.xml.gz | 3.8 KB | Display | |
Data in CIF | 1q4v_validation.cif.gz | 5.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/1q4v ftp://data.pdbj.org/pub/pdb/validation_reports/q4/1q4v | 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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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | The crystallographic asymmetry unit of insulin consists of two monomers each consisting two heterochains. The entry presents coordinates for monomer 1 (chain indicators A and B)and monomer 2 (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 the result of B changed in conformation of the first residues of the B-chain. The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations: -y,x-y,z and -x+y,-x,z |
-Components
#1: Protein/peptide | Mass: 2383.698 Da / Num. of mol.: 2 / Fragment: INSULIN A CHAIN / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Homo Sapiens (human). References: GenBank: AAA59172, UniProt: P01308*PLUS #2: Protein/peptide | Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: INSULIN B CHAIN / Source method: obtained synthetically Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN Homo Sapiens (human). References: GenBank: AAA59172, UniProt: P01308*PLUS #3: Chemical | #4: Chemical | ChemComp-IPH / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Tris, sodium citrate, acetone, phenol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 2001 / Details: mirrors |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.24 Å / Num. obs: 5897 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 43.1 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4.1 / Num. unique all: 543 / % possible all: 89.3 |
Reflection | *PLUS Lowest resolution: 23.2 Å / Num. obs: 5892 |
Reflection shell | *PLUS % possible obs: 89.3 % / Redundancy: 1.27 % / Num. unique obs: 543 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1TRZ Resolution: 2→23.24 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Flat model / Bsol: 37.6603 Å2 / ksol: 0.29202 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→23.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 23.2 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 2.07 Å |