[English] 日本語
Yorodumi
- PDB-5lis: Insulin solved by Native SAD from a dataset collected in one second -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lis
TitleInsulin solved by Native SAD from a dataset collected in one second
Components(Insulin) x 2
KeywordsHYDROLASE / Insulin
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 / negative regulation of glycogen catabolic process / lipid biosynthetic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / positive regulation of cytokine production / acute-phase response / positive regulation of DNA replication / positive regulation of D-glucose import / positive regulation of protein secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / positive regulation of protein localization to nucleus / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / protease binding / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.293 Å
AuthorsCasanas, A. / Finke, A. / Wang, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: EIGER detector: application in macromolecular crystallography.
Authors: Casanas, A. / Warshamanage, R. / Finke, A.D. / Panepucci, E. / Olieric, V. / Noll, A. / Tampe, R. / Brandstetter, S. / Forster, A. / Mueller, M. / Schulze-Briese, C. / Bunk, O. / Wang, M.
History
DepositionJul 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Data collection
Revision 1.3Sep 28, 2016Group: Database references
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Insulin
B: Insulin


Theoretical massNumber of molelcules
Total (without water)5,7882
Polymers5,7882
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-14 kcal/mol
Surface area3460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.870, 76.870, 76.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein/peptide Insulin


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315
#2: Protein/peptide Insulin


Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.55 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionResolution: 2.293→38.44 Å / Num. obs: 5420 / % possible obs: 85 % / Redundancy: 5.4 % / Rrim(I) all: 0.027 / Net I/σ(I): 31.14
Reflection shellHighest resolution: 2.293 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.293→38.44 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.118 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26186 303 10.1 %RANDOM
Rwork0.21697 ---
obs0.22149 2706 85.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 58.996 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.293→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms401 0 0 3 404
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019412
X-RAY DIFFRACTIONr_bond_other_d0.0020.02372
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.942558
X-RAY DIFFRACTIONr_angle_other_deg0.983854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.834549
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47424.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.921564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.774151
X-RAY DIFFRACTIONr_chiral_restr0.0910.261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02466
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02103
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8393.763202
X-RAY DIFFRACTIONr_mcbond_other1.8423.757201
X-RAY DIFFRACTIONr_mcangle_it3.1735.613249
X-RAY DIFFRACTIONr_mcangle_other3.1665.62250
X-RAY DIFFRACTIONr_scbond_it1.5933.995208
X-RAY DIFFRACTIONr_scbond_other1.594209
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6785.938310
X-RAY DIFFRACTIONr_long_range_B_refined4.94644.156459
X-RAY DIFFRACTIONr_long_range_B_other4.94144.203460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.293→2.352 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 11 -
Rwork0.253 88 -
obs--38.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.67321.83252.64995.6151-1.61677.54750.33790.4613-0.7099-0.7768-0.0063-0.34220.61090.5422-0.33160.21290.1157-0.02460.1648-0.02350.17951.259-12.616-19.936
23.2587-1.55190.996310.43292.600914.44940.30030.1209-0.5226-0.0636-0.1165-0.00840.46460.2516-0.18380.04680.0324-0.03560.03510.00520.1095-2.57-6.257-18.544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION2B1 - 30

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

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

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

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

Read more