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- PDB-5hrq: Insulin with proline analog HzP at position B28 in the R6 state -

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Basic information

Entry
Database: PDB / ID: 5hrq
TitleInsulin with proline analog HzP at position B28 in the R6 state
Components
  • Insulin A-Chain
  • Insulin B-Chain
KeywordsHORMONE / Insulin / non-canonical amino acid / hydroxyproline / non-natural amino acid / unnatural amino acid
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / Insulin receptor recycling / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / Insulin receptor recycling / 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 peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / alpha-beta T cell activation / negative regulation of gluconeogenesis / negative regulation of acute inflammatory response / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of dendritic spine maintenance / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of glycogen biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of protein secretion / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / Signal attenuation / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / positive regulation of insulin receptor signaling pathway / Regulation of insulin secretion / endoplasmic reticulum-Golgi intermediate compartment membrane / transport vesicle / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / 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 long-term synaptic potentiation / regulation of transmembrane transporter activity / positive regulation of cell differentiation / regulation of synaptic plasticity / activation of protein kinase B activity / cognition / positive regulation of cytokine production / positive regulation of protein secretion / acute-phase response / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of nitric-oxide synthase activity / hormone activity / insulin receptor binding / vasodilation / insulin receptor signaling pathway / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / regulation of protein localization / glucose metabolic process / glucose homeostasis / cell-cell signaling / 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 / positive regulation of MAPK cascade / protease binding / 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 DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin family signature. / Insulin, conserved site / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å
AuthorsLieblich, S.A. / Fang, K.Y. / Cahn, J.K.B. / Tirrell, D.A.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: J. Am. Chem. Soc. / Year: 2017
Title: 4S-Hydroxylation of Insulin at ProB28 Accelerates Hexamer Dissociation and Delays Fibrillation.
Authors: Lieblich, S.A. / Fang, K.Y. / Cahn, J.K.B. / Rawson, J. / LeBon, J. / Ku, H.T. / Tirrell, D.A.
History
DepositionJan 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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)35,76822
Polymers35,00212
Non-polymers76610
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19620 Å2
ΔGint-236 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.156, 60.680, 60.665
Angle α, β, γ (deg.)90.00, 110.82, 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): CAG18515 / References: UniProt: P01308
#2: Protein/peptide
Insulin B-Chain


Mass: 3449.953 Da / Num. of mol.: 6 / Mutation: Pro28Hzp
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INS / Plasmid: pQE80L / Production host: Escherichia coli (E. coli) / Strain (production host): CAG18515 / References: UniProt: P01308

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Non-polymers , 4 types, 167 molecules

#3: Chemical
ChemComp-IPH / PHENOL / Phenol


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


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 300 mM Tris, 17 mM zinc acetate, 1% phenol, 7.5% acetone, 2.675 M 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: Jun 24, 2015
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: 1.28→56.7 Å / Num. obs: 79335 / % possible obs: 96 % / Redundancy: 3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.028 / Net I/σ(I): 13.6 / Num. measured all: 239532 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.28-1.32.20.4512.1569226130.6780.35962.1
6.88-35.663.30.0393318245600.9890.02699.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
Aimless0.3.11data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→56.7 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.348 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16843 3951 5 %RANDOM
Rwork0.13508 ---
obs0.13672 75363 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.477 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.43 Å2
2---0.41 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.28→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2349 0 46 157 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192574
X-RAY DIFFRACTIONr_bond_other_d0.0080.022322
X-RAY DIFFRACTIONr_angle_refined_deg1.2591.9793485
X-RAY DIFFRACTIONr_angle_other_deg1.12735324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022909
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02653
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_it52.0331247
X-RAY DIFFRACTIONr_mcbond_other5.0132.0281246
X-RAY DIFFRACTIONr_mcangle_it5.6572.9721515
X-RAY DIFFRACTIONr_mcangle_other5.6572.9761516
X-RAY DIFFRACTIONr_scbond_it11.452.5281327
X-RAY DIFFRACTIONr_scbond_other11.4462.5271328
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other13.1693.631955
X-RAY DIFFRACTIONr_long_range_B_refined13.05122.2232448
X-RAY DIFFRACTIONr_long_range_B_other13.04822.222449
X-RAY DIFFRACTIONr_rigid_bond_restr7.27934896
X-RAY DIFFRACTIONr_sphericity_free26.701537
X-RAY DIFFRACTIONr_sphericity_bonded23.67654942
LS refinement shellResolution: 1.278→1.311 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 218 -
Rwork0.206 4122 -
obs--71.57 %

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