|Entry||Database: PDB / ID: 5ena|
|Title||Xray crystal structure of isotope-labeled human insulin|
|Keywords||HORMONE / Isotope-labeled / Human insulin / Chemical protein synthesis / Spontaneous resolution|
|Function / homology|
Function and homology information
Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / regulation of cellular amino acid metabolic process / negative regulation of acute inflammatory response / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / Regulation of insulin secretion / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of insulin receptor signaling pathway / endosome lumen / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / positive regulation of cell differentiation / regulation of transmembrane transporter activity / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of brown fat cell differentiation / regulation of synaptic plasticity / cognition / positive regulation of long-term synaptic potentiation / regulation of protein localization / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / vasodilation / insulin receptor signaling pathway / Golgi lumen / glucose metabolic process / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Golgi membrane / Amyloid fiber formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin family signature. / Insulin, conserved site / Insulin-like superfamily
Similarity search - Domain/homology
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å|
|Authors||Mandal, K. / Dhayalan, B. / Avital-Shmilovici, M. / Tokmakoff, A. / Kent, S.B.H.|
|Funding support|| United States, 1items |
|Citation||Journal: Chembiochem / Year: 2016|
Title: Crystallization of Enantiomerically Pure Proteins from Quasi-Racemic Mixtures: Structure Determination by X-Ray Diffraction of Isotope-Labeled Ester Insulin and Human Insulin.
Authors: Mandal, K. / Dhayalan, B. / Avital-Shmilovici, M. / Tokmakoff, A. / Kent, S.B.
|Structure viewer||Molecule: |
Downloads & links
A: Insulin chain A
B: Insulin chain B
A: Insulin chain A
B: Insulin chain B
A: Insulin chain A
B: Insulin chain B
|Components on special symmetry positions|
|#1: Protein/peptide|| |
Mass: 2383.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
|#2: Protein/peptide|| |
Mass: 3433.953 Da / Num. of mol.: 1 / Mutation: 1-(13C=18O)PheB24 / Source method: obtained synthetically / Details: chemical synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
|#3: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3.39 Å3/Da / Density % sol: 63.72 %|
|Crystal grow||Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 |
Details: 0.1 M HEPES, 0.2 M sodium citrate tribasic dihydrate, 11% MPD
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å|
|Detector||Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2014|
|Radiation||Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.98 Å / Relative weight: 1|
|Reflection||Resolution: 1.35→50 Å / Num. obs: 17473 / % possible obs: 100 % / Redundancy: 19.6 % / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.016 / Rrim(I) all: 0.071 / Χ2: 0.785 / Net I/σ(I): 59.3 / Num. measured all: 342077|
Diffraction-ID: 1 / Rejects: 0
|Phasing||Method: molecular replacement|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 1B2A
Resolution: 1.35→27.554 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 13.21 / Stereochemistry target values: ML
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL|
|Displacement parameters||Biso max: 69.14 Å2 / Biso mean: 27.5288 Å2 / Biso min: 14.04 Å2|
|Refinement step||Cycle: final / Resolution: 1.35→27.554 Å|
|Refine LS restraints|
|LS refinement shell|
Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi