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- PDB-5t7r: A6-A11 trans-dicarba human insulin -

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Basic information

Entry
Database: PDB / ID: 5t7r
TitleA6-A11 trans-dicarba human insulin
Components
  • Insulin A chain
  • Insulin B chain
KeywordsHORMONE / Insulin dicarba bond
Function / homology
Function and homology information


Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process ...Signaling by Insulin receptor / negative regulation of glycogen catabolic process / alpha-beta T cell activation / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of feeding behavior / negative regulation of fatty acid metabolic process / 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 / negative regulation of gluconeogenesis / negative regulation of reactive oxygen species biosynthetic process / positive regulation of cellular protein metabolic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / regulation of cellular amino acid metabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / fatty acid homeostasis / endosome lumen / transport vesicle / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / regulation of transmembrane transporter activity / positive regulation of cell differentiation / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / wound healing / endoplasmic reticulum to Golgi vesicle-mediated transport / positive regulation of MAPK cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Amyloid fiber formation / Golgi membrane / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin-like superfamily / Insulin family signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsMenting, J.G. / Lawrence, M.C. / Robinson, A.J. / Forbes, B.E.
CitationJournal: Sci Rep / Year: 2017
Title: Insulin in motion: The A6-A11 disulfide bond allosterically modulates structural transitions required for insulin activity.
Authors: van Lierop, B. / Ong, S.C. / Belgi, A. / Delaine, C. / Andrikopoulos, S. / Haworth, N.L. / Menting, J.G. / Lawrence, M.C. / Robinson, A.J. / Forbes, B.E.
History
DepositionSep 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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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


Theoretical massNumber of molelcules
Total (without water)11,5634
Polymers11,5634
Non-polymers00
Water1,74797
1
A: Insulin A chain
B: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,7822
Polymers5,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-14 kcal/mol
Surface area3420 Å2
MethodPISA
2
C: Insulin A chain
D: Insulin B chain


Theoretical massNumber of molelcules
Total (without water)5,7822
Polymers5,7822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-16 kcal/mol
Surface area3310 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)77.280, 77.280, 77.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-134-

HOH

21B-136-

HOH

31B-138-

HOH

41D-101-

HOH

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Components

#1: Protein/peptide Insulin A chain


Mass: 2347.622 Da / Num. of mol.: 2 / Mutation: C6(ABA), C11(ABA) / Source method: obtained synthetically
Details: A chain of human insulin with CysA6 and CysA11 replaced with alpha-aminobutyric acid residues with a trans-dicarba bond formed between their respective gamma-carbons
Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin B chain


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.9 M potassium sodium tartrate, 0.1 M Tris HCl pH 8.5, 0.5% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. obs: 22449 / % possible obs: 99.9 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Net I/σ(I): 11.7
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 10.4 % / Rmerge(I) obs: 5.03 / Mean I/σ(I) obs: 0.38 / CC1/2: 0.11 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10pre-2104_1692: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.55→19.32 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2174 1128 5.02 %
Rwork0.1935 --
obs0.1947 22449 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms794 0 0 97 891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006845
X-RAY DIFFRACTIONf_angle_d0.731148
X-RAY DIFFRACTIONf_dihedral_angle_d11.388492
X-RAY DIFFRACTIONf_chiral_restr0.052125
X-RAY DIFFRACTIONf_plane_restr0.004148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5503-1.62080.3781360.36722528X-RAY DIFFRACTION95
1.6208-1.70620.35261410.34042643X-RAY DIFFRACTION100
1.7062-1.8130.35341400.32582655X-RAY DIFFRACTION100
1.813-1.95290.30161350.26232669X-RAY DIFFRACTION100
1.9529-2.14920.21871420.18922665X-RAY DIFFRACTION100
2.1492-2.45960.211430.17772652X-RAY DIFFRACTION100
2.4596-3.09680.18731400.17792720X-RAY DIFFRACTION100
3.0968-19.32150.18791510.16052789X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 97.0259 Å / Origin y: 38.9391 Å / Origin z: -0.7338 Å
111213212223313233
T0.1745 Å20.0055 Å2-0.0014 Å2-0.1715 Å20.0024 Å2--0.1915 Å2
L1.6033 °20.0926 °21.7773 °2-1.8604 °20.0075 °2--7.5727 °2
S-0.0087 Å °-0.0684 Å °-0.0899 Å °0.0669 Å °0.0094 Å °0.0158 Å °0.1151 Å °-0.0429 Å °0.0122 Å °
Refinement TLS groupSelection details: all

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