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- PDB-2ws1: Semi-synthetic analogue of human insulin NMeTyrB26-insulin in mon... -

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Basic information

Entry
Database: PDB / ID: 2ws1
TitleSemi-synthetic analogue of human insulin NMeTyrB26-insulin in monomer form
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / ANALOGUE / DIABETES MELLITUS
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic 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 respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / 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 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / Regulation of insulin secretion / acute-phase response / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of cell differentiation / negative regulation of proteolysis / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / 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 / endoplasmic reticulum lumen / Golgi membrane / 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
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
ACETATE ION / Insulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBrzozowski, A.M. / Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Implications for the Active Form of Human Insulin Based on the Structural Convergence of Highly Active Hormone Analogues.
Authors: Jiracek, J. / Zakova, L. / Antolikova, E. / Watson, C.J. / Turkenburg, J.P. / Dodson, G.G. / Brzozowski, A.M.
History
DepositionSep 3, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Version format compliance
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8913
Polymers5,8322
Non-polymers591
Water73941
1
A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules

A: INSULIN A CHAIN
B: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7816
Polymers11,6634
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+11
Buried area3780 Å2
ΔGint-41 kcal/mol
Surface area6150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.189, 38.189, 124.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

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Components

#1: Protein/peptide INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3447.979 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: METHYLATION OF B26 PEPTIDE NITROGEN ATOM IN B CHAIN OF HUMAN INSULIN
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACETATE (ACT): ACETATE ANION
Sequence detailsN ATOM OF B26 PEPTIDE IS METHYLATED

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 3 / Details: 0.055 M NA2SO4 PH 3.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 6518 / % possible obs: 95.1 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 9.5 / % possible all: 52.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0082refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MSO

1mso


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.642 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. B1 RESIDUE IS NOT MODELLED DUE TO HIGH MOBILITY. B29 AND B30 B CHAIN TERMINAL RESIUDES ARE NOT MODELLED DUE TO HIGH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. B1 RESIDUE IS NOT MODELLED DUE TO HIGH MOBILITY. B29 AND B30 B CHAIN TERMINAL RESIUDES ARE NOT MODELLED DUE TO HIGH MOBILITY. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2477 304 4.7 %RANDOM
Rwork0.18431 ---
obs0.18752 6145 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2--0.71 Å20 Å2
3----1.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms378 0 4 41 423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.021416
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.959571
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.621552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5042520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.731562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.949151
X-RAY DIFFRACTIONr_chiral_restr0.1240.263
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021331
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.7751.5258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.5072417
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7463158
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.544.5154
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.2933416
X-RAY DIFFRACTIONr_sphericity_free8.667341
X-RAY DIFFRACTIONr_sphericity_bonded4.0283404
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 19 -
Rwork0.275 436 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 9.0144 Å / Origin y: -11.3733 Å / Origin z: 54.3555 Å
111213212223313233
T0.0645 Å2-0.0458 Å2-0.0324 Å2-0.1139 Å2-0.0069 Å2--0.075 Å2
L2.4239 °20.4783 °2-0.9989 °2-0.9654 °2-0.4181 °2--3.6037 °2
S0.0025 Å °-0.0905 Å °0.0836 Å °0.0464 Å °-0.0802 Å °0.0439 Å °-0.2344 Å °0.207 Å °0.0777 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION1B2 - 28

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