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- PDB-4ung: Human insulin B26Asn mutant crystal structure -

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Basic information

Entry
Database: PDB / ID: 4ung
TitleHuman insulin B26Asn mutant crystal structure
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / B26 SITE
Function / homology
Function and homology information


negative regulation of glycogen catabolic 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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst ...negative regulation of glycogen catabolic 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 / regulation of protein secretion / Insulin processing / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / activation of protein kinase B activity / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / endosome lumen / positive regulation of long-term synaptic potentiation / acute-phase response / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / wound healing / positive regulation of neuron projection development / hormone activity / negative regulation of protein catabolic process / regulation of synaptic plasticity / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / glucose metabolic process / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / endoplasmic reticulum lumen / Amyloid fiber formation / 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-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: 1.81 Å
AuthorsZakova, L. / Klevtikova, E. / Lepsik, M. / Collinsova, M. / Watson, C.J. / Turkenburg, J.P. / Jiracek, J. / Brzozowski, A.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Human Insulin Analogues Modified at the B26 Site Reveal a Hormone Conformation that is Undetected in the Receptor Complex
Authors: Zakova, L. / Klevtikova, E. / Lepsik, M. / Collinsova, M. / Watson, C.J. / Turkenburg, J.P. / Jiracek, J. / Brzozowski, A.M.
History
DepositionMay 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)11,6335
Polymers11,5374
Non-polymers961
Water2,324129
1
A: INSULIN A CHAIN
B: INSULIN B CHAIN


Theoretical massNumber of molelcules
Total (without water)5,7692
Polymers5,7692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-11.9 kcal/mol
Surface area4010 Å2
MethodPISA
2
C: INSULIN A CHAIN
D: INSULIN B CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8653
Polymers5,7692
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-21.9 kcal/mol
Surface area4000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.630, 45.630, 117.720
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 / Details: SEMISYNTHESISED, NOT RECOMBINANT / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN B CHAIN


Mass: 3384.882 Da / Num. of mol.: 2 / Mutation: YES / Source method: obtained synthetically / Details: SEMISYNTHESISED, NOT RECOMBINANT / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P01308
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.5 Å3/Da / Density % sol: 18 % / Description: NONE
Crystal growpH: 4 / Details: 0.035 M (NH4)2SO4, PH 4.0, CP = 5 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 4, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.81→45.63 Å / Num. obs: 12092 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.1
Reflection shellResolution: 1.81→1.85 Å / Redundancy: 15.6 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 4.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0033refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MSO

1mso


Resolution: 1.81→36.06 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.658 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THERE ARE TWO INSULIN MOLECULES IN THE AU BUT THEY DO NOT REPRESENT ANY PHYSIOLOGICAL ENTITY
RfactorNum. reflection% reflectionSelection details
Rfree0.21992 574 4.8 %RANDOM
Rwork0.17386 ---
obs0.17594 11457 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.849 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2--0.7 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 1.81→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms768 0 5 129 902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.019843
X-RAY DIFFRACTIONr_bond_other_d0.0010.02746
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9481154
X-RAY DIFFRACTIONr_angle_other_deg0.9923.0141707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.67525.34943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48315129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.977152
X-RAY DIFFRACTIONr_chiral_restr0.1250.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021004
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02210
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_it1.8071.768418
X-RAY DIFFRACTIONr_mcbond_other1.7851.763417
X-RAY DIFFRACTIONr_mcangle_it2.7082.616526
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8792.227425
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: 1.806→1.853 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 48 -
Rwork0.198 806 -
obs--99.65 %

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