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- PDB-7ins: STRUCTURE OF PORCINE INSULIN COCRYSTALLIZED WITH CLUPEINE Z -

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Basic information

Entry
Database: PDB / ID: 7ins
TitleSTRUCTURE OF PORCINE INSULIN COCRYSTALLIZED WITH CLUPEINE Z
Components
  • (INSULIN (CHAIN ...) x 2
  • GENERAL PROTAMINE CHAIN
KeywordsHORMONE
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 / positive regulation of fatty acid biosynthetic process / positive regulation of glucose metabolic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / negative regulation of glycogen catabolic process / lipid biosynthetic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / positive regulation of respiratory burst / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / 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 cytokine production / acute-phase response / positive regulation of DNA replication / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / wound healing / 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 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 / negative regulation of gene expression / positive regulation of cell population proliferation / extracellular space / 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
M-CRESOL / Unknown ligand / Insulin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBalschmidt, P. / Hansen, F.B. / Dodson, E. / Dodson, G. / Korber, F.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure of porcine insulin cocrystallized with clupeine Z.
Authors: Balschmidt, P. / Hansen, F.B. / Dodson, E.J. / Dodson, G.G. / Korber, F.
#1: Journal: Nature / Year: 1989
Title: Phenol Stabilizes More Helix in a New Symmetrical Zinc Insulin Hexamer
Authors: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D.
#2: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1988
Title: The Structure of 2Zn Pig Insulin Crystals at 1.5 Angstroms Resolution
Authors: Baker, E.N. / Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.M.C. / Hubbard, R.E. / Isaacs, N.W. / Reynolds, C.D. / Sakabe, K. / Sakabe, N. / Vijayan, N.M.
History
DepositionSep 3, 1991Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Feb 12, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id
Remark 650HELIX THE B CHAIN HELIX IS EXTENDED TO THE FIRST SIX RESIDUES OF THE B CHAIN, THEREBY RUNNING FROM ...HELIX THE B CHAIN HELIX IS EXTENDED TO THE FIRST SIX RESIDUES OF THE B CHAIN, THEREBY RUNNING FROM B 1 TO B 20.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
E: INSULIN (CHAIN A)
F: INSULIN (CHAIN B)
G: GENERAL PROTAMINE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,33913
Polymers18,7437
Non-polymers5966
Water1,964109
1
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
G: GENERAL PROTAMINE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2754
Polymers7,1673
Non-polymers1081
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1676
Polymers5,7882
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-11 kcal/mol
Surface area4270 Å2
MethodPISA
3
E: INSULIN (CHAIN A)
F: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8963
Polymers5,7882
Non-polymers1081
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-11 kcal/mol
Surface area4380 Å2
MethodPISA
4
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
E: INSULIN (CHAIN A)
F: INSULIN (CHAIN B)
G: GENERAL PROTAMINE CHAIN
hetero molecules

A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
E: INSULIN (CHAIN A)
F: INSULIN (CHAIN B)
G: GENERAL PROTAMINE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,67726
Polymers37,48514
Non-polymers1,19212
Water25214
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area27400 Å2
ΔGint-220 kcal/mol
Surface area11820 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-95 kcal/mol
Surface area10940 Å2
MethodPISA
6
G: GENERAL PROTAMINE CHAIN

G: GENERAL PROTAMINE CHAIN

C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules

C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules

E: INSULIN (CHAIN A)
F: INSULIN (CHAIN B)
hetero molecules

E: INSULIN (CHAIN A)
F: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,88620
Polymers25,91010
Non-polymers97610
Water18010
TypeNameSymmetry operationNumber
crystal symmetry operation4_455y-1/2,-x+1/2,z+1/41
crystal symmetry operation6_455x-1/2,-y+1/2,-z+1/41
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
crystal symmetry operation2_555-x,-y,z+1/21
crystal symmetry operation7_555y,x,-z1
Buried area9260 Å2
ΔGint-77 kcal/mol
Surface area19570 Å2
MethodPISA
7
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
hetero molecules

A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7926
Polymers11,5754
Non-polymers2162
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3540 Å2
ΔGint-31 kcal/mol
Surface area6850 Å2
MethodPISA
8
B: INSULIN (CHAIN B)
D: INSULIN (CHAIN B)
F: INSULIN (CHAIN B)
G: GENERAL PROTAMINE CHAIN
hetero molecules

B: INSULIN (CHAIN B)
D: INSULIN (CHAIN B)
F: INSULIN (CHAIN B)
G: GENERAL PROTAMINE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,72614
Polymers23,1838
Non-polymers5436
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area14350 Å2
ΔGint-130 kcal/mol
Surface area12250 Å2
MethodPISA
9
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules

E: INSULIN (CHAIN A)
F: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0639
Polymers11,5754
Non-polymers4885
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3940 Å2
ΔGint-30 kcal/mol
Surface area7050 Å2
MethodPISA
10
B: INSULIN (CHAIN B)
D: INSULIN (CHAIN B)
F: INSULIN (CHAIN B)
G: GENERAL PROTAMINE CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8637
Polymers11,5914
Non-polymers2723
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-50 kcal/mol
Surface area9930 Å2
MethodPISA
11
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules

C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,33512
Polymers11,5754
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3580 Å2
ΔGint-22 kcal/mol
Surface area7320 Å2
MethodPISA
12
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8963
Polymers5,7882
Non-polymers1081
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-10 kcal/mol
Surface area4130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.900, 62.900, 85.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Atom site foot note1: GLY G 21 - GLY G 22 OMEGA ANGLE = 149.010 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: LYS G 33 - GLY G 35 OMEGA ANGLE = 303.917 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

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INSULIN (CHAIN ... , 2 types, 6 molecules ACEBDF

#1: Protein/peptide INSULIN (CHAIN A)


Mass: 2383.698 Da / Num. of mol.: 3
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.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315

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Protein/peptide , 1 types, 1 molecules G

#3: Protein/peptide GENERAL PROTAMINE CHAIN


Mass: 1379.692 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 115 molecules

#4: Chemical ChemComp-CRS / M-CRESOL


Mass: 108.138 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.72 %
Crystal grow
*PLUS
Temperature: 277 K / pH: 7.3 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 Murea11
227 mMphosphoric acid11
321 mMm-cresol11
4120 mM11NaCl
53 mg/mlzinc-free pig insulin11
60.275 mM11ZnCl2

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Data collection

Reflection
*PLUS
% possible obs: 75 % / Rmerge(I) obs: 0.071

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.194 / Highest resolution: 2 Å
Details: CHAIN *G* IS THE GENERAL PROTAMINE CHAIN. THE PROTAMINE RESIDUES HAVE BEEN SELECTED TO FIT THE ELECTRON DENSITY WITHOUT ANY REFERENCE TO THE SEQUENCE OR CONTINUITY OF THE CLUPEINE Z. FOR ...Details: CHAIN *G* IS THE GENERAL PROTAMINE CHAIN. THE PROTAMINE RESIDUES HAVE BEEN SELECTED TO FIT THE ELECTRON DENSITY WITHOUT ANY REFERENCE TO THE SEQUENCE OR CONTINUITY OF THE CLUPEINE Z. FOR THIS REASON SOME ATOMS HAVE ZERO OCCUPANCY. THE SEQRES RECORDS FOR CHAIN *G* PRESENT THE ACTUAL SEQUENCE OF CLUPEINE Z. THE ATOM RECORDS FOR CHAIN *G* HAVE BEEN PRESENTED WITH RESIDUE NAME *UNK*. THE FOLLOWING PROTAMINE RESIDUES BELONG (LOOSELY) TOGETHER: ASSOCIATED WITH THE DIMER-DIMER INTERFACE G41, G 25, G 5, G 6, G 43; ASSOCIATED WITH THE TOP OF THE CENTRAL CAVITY G 8, G 21 - G 23, G 33. G 35 CA, C, O HAVE BEEN FITTED INTO DENSITY FOR THE UNIDENTIFIED ZINC LIGAND, NOTE THE OCCUPANCY FOR THE OTHER ATOMS OF G 35 IS ZERO. THERE IS AN APPROXIMATE THREEFOLD AXIS THROUGH (26.72, 26.72, 0) WITH DIRECTION COSINES (0.543, -0.543, 0.640).
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 40 109 1492
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 10 Å / Num. reflection obs: 11522 / Rfactor obs: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.7 Å2

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