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- PDB-2ins: THE STRUCTURE OF DES-PHE B1 BOVINE INSULIN -

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Entry
Database: PDB / ID: 2ins
TitleTHE STRUCTURE OF DES-PHE B1 BOVINE INSULIN
Components
  • DES-PHE B1 INSULIN (CHAIN A)
  • DES-PHE B1 INSULIN (CHAIN B)
KeywordsHORMONE
Function / homology
Function and homology information


estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / response to butyrate / negative regulation of appetite ...estradiol secretion / positive regulation of blood circulation / negative regulation of lactation / glucose import in response to insulin stimulus / positive regulation of cell maturation / positive regulation of lactation / response to L-arginine / positive regulation of mammary gland epithelial cell proliferation / response to butyrate / negative regulation of appetite / feeding behavior / response to growth hormone / response to food / positive regulation of Rho protein signal transduction / positive regulation of peptide hormone secretion / protein secretion / negative regulation of lipid catabolic process / response to glucose / positive regulation of protein secretion / insulin receptor binding / response to nutrient levels / positive regulation of insulin secretion / hormone activity / glucose metabolic process / glucose homeostasis / response to heat / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of gene expression / negative regulation of apoptotic process / 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
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSmith, G.D. / Duax, W.L. / Dodson, E.J. / Dodson, G.G. / Degraaf, R.A.G. / Reynolds, C.D.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: The Structure of Des-Phe B1 Bovine Insulin
Authors: Smith, G.D. / Duax, W.L. / Dodson, E.J. / Dodson, G.G. / Degraaf, R.A.G. / Reynolds, C.D.
#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
DepositionMay 10, 1982Processing site: BNL
Revision 1.0Aug 5, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 19, 2025Group: Data collection / Refinement description
Category: refine / refine_hist ...refine / refine_hist / software / struct_biol
Item: _refine.ls_d_res_low / _refine_hist.d_res_low ..._refine.ls_d_res_low / _refine_hist.d_res_low / _software.description / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3246
Polymers11,1934
Non-polymers1312
Water3,315184
1
A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules

A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules

A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,97118
Polymers33,57812
Non-polymers3926
Water1629
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18290 Å2
ΔGint-242 kcal/mol
Surface area12530 Å2
MethodPISA
2
A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules

A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules

A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9859
Polymers16,7896
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 area5270 Å2
ΔGint-96 kcal/mol
Surface area10300 Å2
MethodPISA
3
C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules

C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules

C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9859
Polymers16,7896
Non-polymers1963
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5430 Å2
ΔGint-96 kcal/mol
Surface area9810 Å2
MethodPISA
4
A: DES-PHE B1 INSULIN (CHAIN A)
B: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6623
Polymers5,5962
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-15 kcal/mol
Surface area3580 Å2
MethodPISA
5
C: DES-PHE B1 INSULIN (CHAIN A)
D: DES-PHE B1 INSULIN (CHAIN B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6623
Polymers5,5962
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint-14 kcal/mol
Surface area3420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.600, 81.600, 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 - ARG B 22, LYS D 29.
3: SEE REMARK 8.
Components on special symmetry positions
IDModelComponents
11B-1-

ZN

21D-31-

ZN

31B-52-

HOH

41D-133-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.88, -0.48, 0.02), (-0.48, 0.88, -0.02), (-0.01, -0.03, -1))
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 DES-PHE B1 INSULIN (CHAIN A)


Mass: 2339.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P01317
#2: Protein/peptide DES-PHE B1 INSULIN (CHAIN B)


Mass: 3256.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P01317
#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


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal grow
*PLUS
pH: 6.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
20.02 M111.0mlHCl
30.15 Mzinc acetate110.1ml
40.2 Msodium citrate110.5ml
1protein115.5mg
5acetone110.3ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 2722

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Processing

Software
NameClassificationNB
FASTrefinement
FAST-FOURIERrefinement
RefinementResolution: 2.5→5.945 Å
Details: THE FOLLOWING RESIDUES ARE DISORDERED - ARG B 22, LYS D 29. THE MODEL OF THE WATER STRUCTURE OBTAINED FROM THE REFINEMENT OF 2 ZN PORCINE INSULIN AT 1.5 ANGSTROMS RESOLUTION WAS USED ...Details: THE FOLLOWING RESIDUES ARE DISORDERED - ARG B 22, LYS D 29. THE MODEL OF THE WATER STRUCTURE OBTAINED FROM THE REFINEMENT OF 2 ZN PORCINE INSULIN AT 1.5 ANGSTROMS RESOLUTION WAS USED THROUGHOUT THE DES-PHE B1 INSULIN REFINEMENT.
RfactorNum. reflection
Rwork0.18 -
obs-2128
Refinement stepCycle: LAST / Resolution: 2.5→5.945 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms770 0 2 184 956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.2
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg3
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_bond_d / Dev ideal: 0.02

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