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- PDB-9ins: MONOVALENT CATION BINDING IN CUBIC INSULIN CRYSTALS -

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Basic information

Entry
Database: PDB / ID: 9ins
TitleMONOVALENT CATION BINDING IN CUBIC INSULIN CRYSTALS
Components
  • INSULIN (CHAIN A)
  • INSULIN (CHAIN B)
KeywordsHORMONE
Function / homology
Function and homology information


positive regulation of lipoprotein lipase activity / 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 / response to L-arginine ...positive regulation of lipoprotein lipase activity / 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 / response to L-arginine / lactate biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / positive regulation of fatty acid biosynthetic process / glycoprotein biosynthetic process / : / negative regulation of glycogen catabolic process / COPI-mediated anterograde transport / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / lipid biosynthetic process / negative regulation of acute inflammatory response / positive regulation of respiratory burst / alpha-beta T cell activation / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of dendritic spine maintenance / fatty acid homeostasis / positive regulation of glycogen biosynthetic process / positive regulation of insulin receptor signaling pathway / negative regulation of respiratory burst involved in inflammatory response / negative regulation of lipid catabolic process / nitric oxide-cGMP-mediated signaling / regulation of protein localization to plasma membrane / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of mitotic nuclear division / positive regulation of glycolytic process / positive regulation of DNA replication / positive regulation of D-glucose import across plasma membrane / acute-phase response / positive regulation of protein secretion / positive regulation of cytokine production / wound healing / insulin receptor binding / negative regulation of protein catabolic process / hormone activity / positive regulation of protein localization to nucleus / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / protease binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / positive regulation of cell population proliferation / : / 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 speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsBadger, J. / Dodson, G.G.
Citation
Journal: Biophys.J. / Year: 1992
Title: Monovalent cation binding to cubic insulin crystals
Authors: Gursky, O. / Li, Y. / Badger, J. / Caspar, D.L.D.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure of the Pig Insulin Dimer in the Cubic Crystal
Authors: Badger, J. / Harris, M.R. / Reynolds, C.D. / Evans, A.C. / Dodson, E.J. / Dodson, G.G. / North, A.C.T.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991
Title: Water Structure in Cubic Insulin Crystals
Authors: Badger, J. / Caspar, D.L.D.
#3: Journal: J.Mol.Biol. / Year: 1978
Title: Zinc-Free Cubic Pig Insulin: Crystallization and Structure Determination
Authors: Dodson, E.J. / Dodson, G.G. / Lewitova, A. / Sabesan, M.
History
DepositionOct 23, 1991Processing site: BNL
Revision 1.0Nov 7, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)5,7882
Polymers5,7882
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-13 kcal/mol
Surface area3410 Å2
MethodPISA
2
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)

A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)


Theoretical massNumber of molelcules
Total (without water)11,5754
Polymers11,5754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_565x,-y+1,-z+1/21
Buried area4350 Å2
ΔGint-35 kcal/mol
Surface area5560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.900, 78.900, 78.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Atom site foot note1: WATER 24 IS PROBABLY A PARTIALLY OCCUPIED SODIUM ION. ANOTHER SODIUM SITE WITH VERY LOW OCCUPANCY OVERLAPS THE MAJOR CONFORMATION OF HIS B10 (SEE REF 3).
2: SEE REMARK 5.
Components on special symmetry positions
IDModelComponents
11B-44-

HOH

21B-64-

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.) Sus scrofa (pig) / References: UniProt: P01315
#2: Protein/peptide INSULIN (CHAIN B)


Mass: 3403.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.21 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails (eV)
115 mg/mlbovine insulin11
20.018 Msodium phosphate11
30.01 Msodium-EDTA11pH10.5
40.15 Msodium phosphate12
50.01 Msodium-EDTA12
60.5 %(w/v)xylene12pH9.2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→10 Å / Rfactor obs: 0.178 / σ(F): 2
Details: BY COMPARISON WITH MULTIPLE DATA SETS FROM BOVINE CUBIC INSULIN COLLECTED IN THE PH RANGE 7 TO 11 (REFERENCE 1 AND UNPUBLISHED RESULTS) IT HAS BEEN POSSIBLE TO RELIABLY IDENTIFY ADDITIONAL ...Details: BY COMPARISON WITH MULTIPLE DATA SETS FROM BOVINE CUBIC INSULIN COLLECTED IN THE PH RANGE 7 TO 11 (REFERENCE 1 AND UNPUBLISHED RESULTS) IT HAS BEEN POSSIBLE TO RELIABLY IDENTIFY ADDITIONAL CONFORMATIONS FOR SEVERAL SIDE CHAINS THAT WERE NOT INCLUDED IN THE PUBLISHED (ACTA CRYSTALLOGR.) REPORT. THESE HAVE BEEN MODELED, THE ORDERED SOLVENT RATIONALIZED AND THE STRUCTURE REFINED FURTHER. THE R-FACTOR AND STEREOCHEMICAL PARAMETERS IN THIS ENTRY ARE FOR THIS NEW MODEL. IN THE ACTA CRYSTALLOGRAPHICA 1991 PUBLICATION (REFERENCE 2 ABOVE) REFERENCE IS MADE TO PROTEIN DATA BANK ENTRY 5INS. THE COORDINATES IN THIS ENTRY SUPERSEDE 5INS.
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms451 0 0 81 532
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1430.15
X-RAY DIFFRACTIONp_singtor_nbd0.1670.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.13
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS

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