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- PDB-4a7e: X-ray crystal structure of porcine insulin flash-cooled at high p... -

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Basic information

Entry
Database: PDB / ID: 4a7e
TitleX-ray crystal structure of porcine insulin flash-cooled at high pressure
Components
  • INSULIN A CHAIN
  • INSULIN B CHAIN
KeywordsHORMONE / HIGH-PRESSURE COOLING / HIGH-PRESSURE PROTEIN CRYSTALLOGRAPHY
Function / homology
Function and homology information


Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine ...Insulin processing / IRS activation / Signal attenuation / Insulin receptor signalling cascade / Signaling by Insulin receptor / Synthesis, secretion, and deacylation of Ghrelin / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Insulin receptor recycling / glycoprotein biosynthetic process / response to L-arginine / positive regulation of lipoprotein lipase activity / lactate biosynthetic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / COPI-mediated anterograde transport / lipid biosynthetic process / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of DNA replication / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / negative regulation of lipid catabolic process / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / glucose homeostasis / insulin receptor signaling pathway / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.856 Å
AuthorsBurkhardt, A. / Warmer, M. / Panneerselvam, S. / Wagner, A. / Reimer, R. / Hohenberg, H. / Meents, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Fast High-Pressure Freezing of Protein Crystals in Their Mother Liquor
Authors: Burkhardt, A. / Warmer, M. / Pannerselvam, S. / Wagner, A. / Zouni, A. / Reimer, R. / Hohenberg, H. / Meents, A.
History
DepositionNov 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Other
Revision 1.2May 30, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)5,7882
Polymers5,7882
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-14.3 kcal/mol
Surface area3200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.100, 77.100, 77.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-2013-

HOH

21B-2001-

HOH

31B-2012-

HOH

41B-2013-

HOH

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Components

#1: Protein/peptide INSULIN A CHAIN


Mass: 2383.698 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: P01315
#2: Protein/peptide INSULIN B CHAIN


Mass: 3403.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: P01315
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.3 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growpH: 10 / Details: 0.5 M SODIUM PHOSPHATE, 0.01 M EDTA, PH 10.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9253
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9253 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 6692 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 10.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 9INS

9ins


Resolution: 1.856→19.275 Å / SU ML: 0.44 / σ(F): 1.99 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2175 923 14.01 %
Rwork0.1761 --
obs0.1818 6589 99.83 %
Solvent computationShrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.344 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.856→19.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms388 0 0 55 443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015400
X-RAY DIFFRACTIONf_angle_d1.51537
X-RAY DIFFRACTIONf_dihedral_angle_d14.882135
X-RAY DIFFRACTIONf_chiral_restr0.09260
X-RAY DIFFRACTIONf_plane_restr0.00868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8558-1.95360.33821220.2627801X-RAY DIFFRACTION100
1.9536-2.07580.25681450.2285790X-RAY DIFFRACTION100
2.0758-2.23590.23521380.1756794X-RAY DIFFRACTION1.01
2.2359-2.46050.22511340.1823800X-RAY DIFFRACTION100
2.4605-2.81560.22231210.1741817X-RAY DIFFRACTION100
2.8156-3.54370.25291310.1806817X-RAY DIFFRACTION100
3.5437-19.2760.16781320.1518847X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1514-0.34410.49491.9571-0.50652.2956-0.03540.33420.0274-0.7064-0.1639-0.7026-0.13450.4070.15690.39680.03990.0810.21260.03010.4638-0.1061-7.0222-21.3983
22.8292-1.1114-1.0353.9976-0.59831.69370.1697-0.26770.3425-0.1824-0.0736-0.1025-0.1962-0.0688-0.10640.2555-0.0075-0.01290.1674-0.01640.3378-2.692-11.9434-15.0638
37.8951-2.03614.00542.44322.22317.6120.07910.76020.278-1.0588-0.2486-0.1312-0.7190.60340.0990.46080.12760.06550.1610.09760.38083.1255-15.3725-23.7797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 1:22)
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 23:30)

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