|Entry||Database: PDB / ID: 4m4h|
|Title||Radiation damage study of Cu T6-insulin - 0.06 MGy|
|Components||(Insulin) x 2|
|Keywords||HORMONE / Copper binding|
|Function / homology|
Function and homology information
glucose import in response to insulin stimulus / response to butyrate / negative regulation of lactation / estradiol secretion / positive regulation of blood circulation / positive regulation of lactation / positive regulation of cell maturation / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to L-arginine ...glucose import in response to insulin stimulus / response to butyrate / negative regulation of lactation / estradiol secretion / positive regulation of blood circulation / positive regulation of lactation / positive regulation of cell maturation / positive regulation of mammary gland epithelial cell proliferation / negative regulation of appetite / response to L-arginine / feeding behavior / response to food / positive regulation of Rho protein signal transduction / response to growth hormone / positive regulation of peptide hormone secretion / protein secretion / positive regulation of insulin secretion / negative regulation of lipid catabolic process / positive regulation of protein secretion / response to glucose / response to nutrient levels / hormone activity / insulin receptor binding / glucose metabolic process / response to heat / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin-like / Insulin, conserved site / Insulin-like superfamily / Insulin family signature.
Similarity search - Domain/homology
COPPER (II) ION / Insulin
Similarity search - Component
|Biological species||Bos taurus (cattle)|
|Method||X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å|
|Authors||Frankaer, C.G. / Harris, P. / Stahl, K.|
|Citation||Journal: Acta Crystallogr.,Sect.D / Year: 2014|
Title: Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T6 bovine insulin derivatives.
Authors: Frankaer, C.G. / Mossin, S. / Stahl, K. / Harris, P.
|Structure viewer||Molecule: |
Downloads & links
|Components on special symmetry positions|
Mass: 2339.645 Da / Num. of mol.: 2 / Fragment: INSULIN A CHAIN (UNP RESIDUES 85-105) / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
Mass: 3403.927 Da / Num. of mol.: 2 / Fragment: INSULIN B CHAIN (UNP RESIDUES 25-54) / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P01317
|#3: Chemical||#4: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 1.82 Å3/Da / Density % sol: 32.29 %|
|Crystal grow||Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.1 |
Details: 0.05M sodium citrate, 15%(v/v) acetone, 7.5mM copper(II)acetate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å|
|Detector||Type: AGILENT ATLAS CCD / Detector: CCD / Date: Jun 14, 2013|
|Radiation||Monochromator: Multilayered mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 1.5418 Å / Relative weight: 1|
|Reflection||Resolution: 1.9→16.75 Å / Num. all: 6370 / Num. obs: 6342 / % possible obs: 99.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -3|
|Reflection shell||Resolution: 1.9→1.97 Å / % possible all: 99.1|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→16.75 Å / SU ML: 0.22 / σ(F): 2.01 / Phase error: 26.2 / Stereochemistry target values: ML|
|Solvent computation||Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL|
|Refinement step||Cycle: LAST / Resolution: 1.9→16.75 Å|
|Refine LS restraints|
|LS refinement shell|
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
-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