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- PDB-3zs2: TyrB25,NMePheB26,LysB28,ProB29-insulin analogue crystal structure -

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Basic information

Entry
Database: PDB / ID: 3zs2
TitleTyrB25,NMePheB26,LysB28,ProB29-insulin analogue crystal structure
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / CARBOHYDRATE METABOLISM / GLUCOSE METABOLISM / DIABETES MELLITUS
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / IRS activation / Insulin processing / 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 respiratory burst / positive regulation of peptide hormone secretion / negative regulation of respiratory burst involved in inflammatory response / negative regulation of gluconeogenesis / positive regulation of protein metabolic process => GO:0051247 / negative regulation of acute inflammatory response / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / COPI-mediated anterograde transport / positive regulation of glycogen biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Signal attenuation / negative regulation of protein secretion / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of nitric oxide mediated signal transduction / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / Regulation of insulin secretion / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / transport vesicle / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / positive regulation of cell differentiation / regulation of transmembrane transporter activity / positive regulation of long-term synaptic potentiation / regulation of synaptic plasticity / cognition / activation of protein kinase B activity / positive regulation of cytokine production / positive regulation of protein secretion / positive regulation of glucose import / positive regulation of nitric-oxide synthase activity / acute-phase response / negative regulation of proteolysis / hormone activity / vasodilation / insulin receptor binding / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / glucose metabolic process / regulation of protein localization / cell-cell signaling / glucose homeostasis / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / protease binding / positive regulation of MAPK cascade / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / negative regulation of gene expression / endoplasmic reticulum lumen / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of transcription, DNA-templated / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin-like / Insulin family signature. / Insulin-like superfamily / Insulin, conserved site
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsAntolikova, E. / Zakova, L. / Turkenburg, J.P. / Watson, C.J. / Hanclova, I. / Sanda, M. / Cooper, A. / Kraus, T. / Brzozowski, A.M. / Jiracek, J.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Non-Equivalent Role of Inter- and Intramolecular Hydrogen Bonds in the Insulin Dimer Interface.
Authors: Antolikova, E. / Zakova, L. / Turkenburg, J.P. / Watson, C.J. / Hanclova, I. / Sanda, M. / Cooper, A. / Kraus, T. / Brzozowski, A.M. / Jiracek, J.A.
History
DepositionJun 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Atomic model
Revision 1.2Oct 26, 2011Group: Database references
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / pdbx_database_status / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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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
E: INSULIN A CHAIN
F: INSULIN B CHAIN
G: INSULIN A CHAIN
H: INSULIN B CHAIN
I: INSULIN A CHAIN
J: INSULIN B CHAIN
K: INSULIN A CHAIN
L: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,75622
Polymers34,99012
Non-polymers76610
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17880 Å2
ΔGint-225.1 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.660, 62.170, 46.678
Angle α, β, γ (deg.)90.00, 111.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein/peptide , 2 types, 12 molecules ACEGIKBDFHJL

#1: Protein/peptide
INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 6 / Mutation: YES / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#2: Protein/peptide
INSULIN B CHAIN


Mass: 3447.980 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308

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Non-polymers , 4 types, 160 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H6O
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE N-PEPTIDE ATOM OF B26PHE IS METHYLATED PHEB25 IS MUTATED TO TYR B28PRO AND B29LYS ARE SWAPPED

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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: 2.4 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 8.2
Details: 0.1 M NACITRATE, 0.3 M TRIS PH 8.2, 0.6 MM ZN(AC)2, 0.06% PHENOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.0712
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0712 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 18615 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.5
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 8.5 / % possible all: 61.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MS0

1ms0


Resolution: 1.97→53.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.412 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.21 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25211 1013 5.2 %RANDOM
Rwork0.19276 ---
obs0.19588 18615 89.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.213 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å21.03 Å2
2---1.18 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.97→53.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 46 150 2440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212343
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9613165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8255271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69624.655116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.38115357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.507156
X-RAY DIFFRACTIONr_chiral_restr0.150.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021788
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.971→2.022 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 48 -
Rwork0.231 829 -
obs--55.68 %

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