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- PDB-5uoz: Insulin with proline analog FyP at position B28 in the T2 state -

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Basic information

Entry
Database: PDB / ID: 5uoz
TitleInsulin with proline analog FyP at position B28 in the T2 state
Components
  • Insulin Chain A
  • Insulin Chain B
KeywordsHORMONE / Insulin
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 / cell-cell signaling / glucose homeostasis / 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: 1.17463871031 Å
AuthorsLieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Insulin with proline analog FyP at position B28 in the T2 state
Authors: Lieblich, S.A. / Fang, K.Y. / Tirrell, D.A.
History
DepositionFeb 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 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 Chain A
B: Insulin Chain B


Theoretical massNumber of molelcules
Total (without water)5,8362
Polymers5,8362
Non-polymers00
Water1,29772
1
A: Insulin Chain A
B: Insulin Chain B

A: Insulin Chain A
B: Insulin Chain B


Theoretical massNumber of molelcules
Total (without water)11,6714
Polymers11,6714
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554x,-y,-z-1/21
Buried area4150 Å2
ΔGint-37 kcal/mol
Surface area5570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.0936, 78.0936, 78.0936
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number199
Space group name H-MI213
Space group name HallI2b2c3
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z+1/2,x
#5: z,-x,-y+1/2
#6: -y+1/2,z,-x
#7: -z,-x+1/2,y
#8: -z+1/2,x,-y
#9: y,-z,-x+1/2
#10: x,-y,-z+1/2
#11: -x+1/2,y,-z
#12: -x,-y+1/2,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1,x+1/2
#17: z+1/2,-x+1/2,-y+1
#18: -y+1,z+1/2,-x+1/2
#19: -z+1/2,-x+1,y+1/2
#20: -z+1,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1
#22: x+1/2,-y+1/2,-z+1
#23: -x+1,y+1/2,-z+1/2
#24: -x+1/2,-y+1,z+1/2
Components on special symmetry positions
IDModelComponents
11A-130-

HOH

21B-128-

HOH

31B-141-

HOH

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Components

#1: Protein/peptide Insulin Chain A


Mass: 2383.698 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#2: Protein/peptide Insulin Chain B


Mass: 3451.944 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Production host: Escherichia coli (E. coli) / References: UniProt: P01308
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 3.46 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 0.3M Tris, 0.5mM Zinc Acetate, 425mM Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2016
RadiationMonochromator: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.175→31.882 Å / Num. obs: 26219 / % possible obs: 98.81 % / Redundancy: 8.9 % / Biso Wilson estimate: 11.9674972676 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 18.03
Reflection shellResolution: 1.175→1.217 Å / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 3.88 / % possible all: 89.84

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T2A

3t2a


Resolution: 1.17463871031→31.8815786962 Å / SU ML: 0.079372996774 / Cross valid method: FREE R-VALUE / σ(F): 1.34757049606 / Phase error: 14.7822322351
RfactorNum. reflection% reflection
Rfree0.154946032189 1250 4.76771683576 %
Rwork0.140917281737 --
obs0.141607998932 26218 98.8053514226 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 20.6373690427 Å2
Refinement stepCycle: LAST / Resolution: 1.17463871031→31.8815786962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms398 0 0 72 470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142122575647423
X-RAY DIFFRACTIONf_angle_d1.37300424535573
X-RAY DIFFRACTIONf_chiral_restr0.073950874262266
X-RAY DIFFRACTIONf_plane_restr0.0059984907369172
X-RAY DIFFRACTIONf_dihedral_angle_d14.91155355147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1746-1.22170.1934579048591350.1783947307682509X-RAY DIFFRACTION90.8591065292
1.2217-1.27730.1734108918791420.1500384165772773X-RAY DIFFRACTION100
1.2773-1.34460.1565445444641290.1378680222532794X-RAY DIFFRACTION99.3879632778
1.3446-1.42890.1443373252941380.1174224339842779X-RAY DIFFRACTION100
1.4289-1.53920.1477659496311440.1158294059682772X-RAY DIFFRACTION99.6582365003
1.5392-1.69410.129324576591610.1184906353672792X-RAY DIFFRACTION99.8309668695
1.6941-1.93920.1466482740591080.129772103112829X-RAY DIFFRACTION99.6268656716
1.9392-2.4430.1462937707991250.1524565960682846X-RAY DIFFRACTION100
2.443-31.89330.1634365038891680.1470900499132874X-RAY DIFFRACTION99.77041653

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