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- PDB-2wrx: Semi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0 -

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Basic information

Entry
Database: PDB / ID: 2wrx
TitleSemi-synthetic analogue of human insulin NMeAlaB26-insulin at pH 3.0
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / ANALOGUE / DIABETES MELLITUS
Function / homology
Function and homology information


: / negative regulation of glycogen catabolic process / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of feeding behavior / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of acute inflammatory response ...: / negative regulation of glycogen catabolic process / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / negative regulation of feeding behavior / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / positive regulation of respiratory burst / alpha-beta T cell activation / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of dendritic spine maintenance / fatty acid homeostasis / positive regulation of brown fat cell differentiation / positive regulation of glycogen biosynthetic process / positive regulation of insulin receptor signaling pathway / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / nitric oxide-cGMP-mediated signaling / regulation of protein localization to plasma membrane / transport vesicle / Insulin receptor recycling / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of D-glucose import across plasma membrane / positive regulation of mitotic nuclear division / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / Insulin receptor signalling cascade / endosome lumen / positive regulation of protein secretion / acute-phase response / positive regulation of cytokine production / wound healing / insulin receptor binding / positive regulation of long-term synaptic potentiation / positive regulation of neuron projection development / glucose metabolic process / positive regulation of cell differentiation / negative regulation of protein catabolic process / Regulation of insulin secretion / regulation of synaptic plasticity / hormone activity / positive regulation of protein localization to nucleus / vasodilation / Golgi lumen / cognition / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / cell-cell signaling / positive regulation of cell growth / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / secretory granule lumen / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / Amyloid fiber formation / receptor ligand activity / negative regulation of gene expression / Golgi membrane / positive regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / : / extracellular region / 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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5025
Polymers11,4794
Non-polymers231
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-46.3 kcal/mol
Surface area6120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.239, 39.239, 124.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein/peptide INSULIN A CHAIN


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


Mass: 3355.884 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically
Details: METHYLATION OF B26 AND D26 PEPTIDE NITROGEN ATOM IN B AND D CHAIN OF HUMAN INSULIN
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN B, TYR 50 TO MAA ENGINEERED RESIDUE IN CHAIN D, TYR 50 TO MAA
Has protein modificationY
Nonpolymer detailsSODIUM (NA): SODIUM CATION
Sequence details26 TYR MUTATED TO ALA AND N ATOM OF B26 PEPTIDE IS METHYLATED 26 TYR MUTATED TO ALA AND N ATOM OF ...26 TYR MUTATED TO ALA AND N ATOM OF B26 PEPTIDE IS METHYLATED 26 TYR MUTATED TO ALA AND N ATOM OF D26 PEPTIDE IS METHYLATED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 3 / Details: 0.18 M LI2SO4, 0.1M NA ACETATE PH 3.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1.0723
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 17552 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.5 / % possible all: 60.5

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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: 1.5→37.42 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.273 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. B1 PHE IS NOT MODELLED. B29 LYS AND B30 THR ARE NOT MODELLED. B21 GLU SIDE CHAIN IS MOBILE AND ITS OCCUPANCY IS SET ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY. B1 PHE IS NOT MODELLED. B29 LYS AND B30 THR ARE NOT MODELLED. B21 GLU SIDE CHAIN IS MOBILE AND ITS OCCUPANCY IS SET TO ZERO. B22 ARG SIDE CHAIN IS MOBILE AND ITS OCCUPANCY IS SET TO ZERO. D1 PHE IS NOT MODELLED. D29 LYS AND D30 THR ARE NOT MODELLED. D21 GLU SIDE CHAIN IS MOBILE AND ITS OCCUPANCY IS SET TO ZERO. D22 ARG SIDE CHAIN IS MOBILE AND ITS OCCUPANCY IS SET TO ZERO.
RfactorNum. reflection% reflectionSelection details
Rfree0.25053 787 5 %RANDOM
Rwork0.18019 ---
obs0.18343 14801 94.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.567 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms742 0 1 101 844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.022767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.981.9541051
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2225100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.86225.29434
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36215114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.593151
X-RAY DIFFRACTIONr_chiral_restr0.1460.2122
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02581
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_it1.981.5485
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8262777
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8773282
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.544.5270
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.2913767
X-RAY DIFFRACTIONr_sphericity_free8.4543102
X-RAY DIFFRACTIONr_sphericity_bonded5.5353745
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 33 -
Rwork0.283 649 -
obs--57.7 %
Refinement TLS params.

T33: 0.0272 Å2 / 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)Origin x (Å)Origin y (Å)Origin z (Å)
10.89-1.03870.31885.8128-1.48723.1336-0.2104-0.07730.03810.25350.30010.1191-0.0732-0.3912-0.08970.06710.0413-0.01360.0871-0.0042.977617.963724.458
21.6061-0.01110.19283.2814-2.20175.0776-0.0731-0.12650.0015-0.25690.1590.16460.3006-0.599-0.08590.0922-0.07-0.00220.1154-0.00831.920219.72968.1554
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 21
2X-RAY DIFFRACTION1B2 - 29
3X-RAY DIFFRACTION2C1 - 21
4X-RAY DIFFRACTION2D2 - 28

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