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- PDB-4ins: THE STRUCTURE OF 2ZN PIG INSULIN CRYSTALS AT 1.5 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 4ins
TitleTHE STRUCTURE OF 2ZN PIG INSULIN CRYSTALS AT 1.5 ANGSTROMS RESOLUTION
Components
  • INSULIN (CHAIN A)
  • INSULIN (CHAIN B)
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 / 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 / Resolution: 1.5 Å
AuthorsDodson, G.G. / Dodson, E.J. / Hodgkin, D.C. / Isaacs, N.W. / Vijayan, M.
Citation
#1: Journal: Proc.R.Soc.London,Ser.B / Year: 1983
Title: A Comparative Assessment of the Zinc-Protein Coordination in 2Zn-Insulin as Determined by X-Ray Absorption Fine Structure (Exafs) and X-Ray Crystallography
Authors: Bordas, J. / Dodson, G.G. / Grewe, H. / Koch, M.H.J. / Krebs, B. / Randall, J.
#2: Journal: Can.J.Biochem. / Year: 1979
Title: Structural Relationships in the Two-Zinc Insulin Hexamer
Authors: Dodson, E.J. / Dodson, G.G. / Hodgkin, D.C. / Reynolds, C.D.
#3: Journal: Acta Crystallogr.,Sect.A / Year: 1978
Title: Experience with Fast Fourier Least Squares in the Refinement of the Crystal Structure of Rhombohedral 2-Zinc Insulin at 1.5 Angstroms Resolution
Authors: Isaacs, N.W. / Agarwal, R.C.
#4: Journal: J.Mol.Biol. / Year: 1978
Title: Rhombohedral Insulin Crystal Transformation
Authors: Bentley, G. / Dodson, G. / Lewitova, A.
#5: Journal: Acta Crystallogr.,Sect.A / Year: 1976
Title: A Method for Fitting Satisfactory Models to Sets of Atomic Positions in Protein Structure Refinements
Authors: Dodson, E.J. / Isaacs, N.W. / Rollett, J.S.
#6: Journal: J.Endocrinol. / Year: 1974
Title: Varieties of Insulin
Authors: Hodgkin, D.C.
#7: Journal: Dan.Tidsskr.Farm. / Year: 1972
Title: The Structure of Insulin
Authors: Hodgkin, D.C.
#8: Journal: Adv.Protein Chem. / Year: 1972
Title: Insulin. The Structure in the Crystal and its Reflection in Chemistry and Biology
Authors: Blundell, T. / Dodson, G. / Hodgkin, D. / Mercola, D.
#9: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1972
Title: The Crystal Structure of Rhombohedral 2 Zinc Insulin
Authors: Blundell, T.L. / Cutfield, J.F. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.C. / Mercola, D.A.
#10: Journal: Nature / Year: 1971
Title: Atomic Positions in Rhombohedral 2-Zinc Insulin Crystals
Authors: Blundell, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.C. / Mercola, D.A. / Vijayan, M.
#11: Journal: Recent Prog.Horm.Res. / Year: 1971
Title: X-Ray Analysis and the Structure of Insulin
Authors: Blundell, T.L. / Dodson, G.G. / Dodson, E. / Hodgkin, D.C. / Vijayan, M.
#12: Journal: J.Mol.Biol. / Year: 1970
Title: X-Ray Diffraction Data on Some Crystalline Varieties of Insulin
Authors: Baker, E.N. / Dodson, G.
#13: Journal: Nature / Year: 1969
Title: Structure of Rhombohedral 2 Zinc Insulin Crystals
Authors: Adams, M.J. / Blundell, T.L. / Dodson, E.J. / Dodson, G.G. / Vijayan, M. / Baker, E.N. / Harding, M.M. / Hodgkin, D.C. / Rimmer, B. / Sheat, S.
#14: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionJul 10, 1989Processing site: BNL
SupersessionApr 15, 1990ID: 1INS
Revision 1.0Apr 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7066
Polymers11,5754
Non-polymers1312
Water6,305350
1
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8533
Polymers5,7882
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-15 kcal/mol
Surface area3790 Å2
MethodPISA
2
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8533
Polymers5,7882
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-15 kcal/mol
Surface area3620 Å2
MethodPISA
3
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)35,11818
Polymers34,72612
Non-polymers3926
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20600 Å2
ΔGint-260 kcal/mol
Surface area12080 Å2
MethodPISA
4
C: INSULIN (CHAIN A)
D: INSULIN (CHAIN B)
hetero molecules

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)17,5599
Polymers17,3636
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5730 Å2
ΔGint-95 kcal/mol
Surface area10440 Å2
MethodPISA
5
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
hetero molecules

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)17,5599
Polymers17,3636
Non-polymers1963
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5580 Å2
ΔGint-95 kcal/mol
Surface area10930 Å2
MethodPISA
6
A: INSULIN (CHAIN A)
B: INSULIN (CHAIN B)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)11,7066
Polymers11,5754
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area5120 Å2
ΔGint-45 kcal/mol
Surface area5710 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-40 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.500, 82.500, 34.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Atom site foot note1: THE QUASI-TWO-FOLD SYMMETRY BREAKS DOWN MOST SERIOUSLY AT RESIDUES GLY A 1 TO GLN A 5 AND GLY C 1 TO GLN C 5 HIS B 5 AND HIS D 5 PHE B 25 AND PHE D 25
2: THE FOLLOWING RESIDUES ARE DISORDERED - GLN B 4, VAL B 12, GLU B 21, ARG B 22, ARG D 22, LYS D 29.
3: SEE REMARK 8.
Components on special symmetry positions
IDModelComponents
11B-101-

ZN

21D-101-

ZN

31B-224-

HOH

41B-245-

HOH

51D-323-

HOH

61D-403-

HOH

71D-455-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.87862, -0.47696, 0.02305), (-0.47743, 0.87837, -0.02286), (-0.00935, -0.03109, -0.99947))
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MOLECULES EACH CONSISTING OF TWO CHAINS. THIS ENTRY PRESENTS COORDINATES FOR MOLECULES I (CHAIN INDICATORS *A* AND *B*) AND II (CHAIN INDICATORS *C* AND *D*). THE QUASI-TWO-FOLD AXIS THAT TRANSFORMS MOLECULE I INTO MOLECULE II IS GIVEN IN THE *MTRIX* RECORDS BELOW. APPLYING THE THREE-FOLD CRYSTALLOGRAPHIC AXIS YIELDS A HEXAMER AROUND THE AXIS. THERE ARE TWO ZINC IONS SITUATED ON THIS THREE-FOLD AXIS. COORDINATES FOR THE ZINC IONS AND SOME WATER MOLECULES ARE INCLUDED BELOW WITH A BLANK CHAIN INDICATOR.

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Components

#1: Protein/peptide INSULIN (CHAIN A)


Mass: 2383.698 Da / Num. of mol.: 2
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / References: UniProt: P01315
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.05 %
Crystal grow
*PLUS
pH: 6.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.02 Mhydrochrolic acid110.5 ml
20.12 Mzinc sulphate110.5 ml
30.2 Mtrisodium citrate112.5 ml
4acetone111.5ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.153 / Highest resolution: 1.5 Å
Details: SOME RESIDUES ARE APPARENTLY DISORDERED BUT DIFFICULT TO DESCRIBE IN TERMS OF ATOMIC POSITIONS. ALA B 30 IS ONE OF THESE RESIDUES. THE FOLLOWING RESIDUES ARE DISORDERED - GLN B 4, VAL B 12, ...Details: SOME RESIDUES ARE APPARENTLY DISORDERED BUT DIFFICULT TO DESCRIBE IN TERMS OF ATOMIC POSITIONS. ALA B 30 IS ONE OF THESE RESIDUES. THE FOLLOWING RESIDUES ARE DISORDERED - GLN B 4, VAL B 12, GLU B 21, ARG B 22, ARG D 22, LYS D 29.
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 2 350 1158
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.005
X-RAY DIFFRACTIONp_angle_deg5.9
Refinement
*PLUS
Num. reflection obs: 10119 / σ(I): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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