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- PDB-3ins: STRUCTURE OF INSULIN. RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT -

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Basic information

Entry
Database: PDB / ID: 3ins
TitleSTRUCTURE OF INSULIN. RESULTS OF JOINT NEUTRON AND X-RAY REFINEMENT
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 / glycoprotein biosynthetic process ...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 / glycoprotein biosynthetic process / response to L-arginine / lactate biosynthetic process / positive regulation of glucose metabolic process / positive regulation of fatty acid biosynthetic process / lipoprotein biosynthetic process / COPI-mediated anterograde transport / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / lipid biosynthetic process / positive regulation of respiratory burst / negative regulation of acute inflammatory response / 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 insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / 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 / positive regulation of DNA replication / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / insulin receptor binding / wound healing / hormone activity / negative regulation of protein catabolic process / positive regulation of protein localization to nucleus / vasodilation / glucose metabolic process / 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
DEUTERATED WATER / Insulin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / Resolution: 1.5 Å
AuthorsWlodawer, A. / Savage, H.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1989
Title: Structure of insulin: results of joint neutron and X-ray refinement.
Authors: Wlodawer, A. / Savage, H. / Dodson, G.
#1: 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.
History
DepositionOct 14, 1988Processing site: BNL
Revision 1.0Jan 9, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Data collection / Non-polymer description / 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 1.4Nov 6, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)11,7066
Polymers11,5754
Non-polymers1312
Water5,855325
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 area1710 Å2
ΔGint-17 kcal/mol
Surface area3860 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 area1760 Å2
ΔGint-17 kcal/mol
Surface area3720 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 area21250 Å2
ΔGint-268 kcal/mol
Surface area12110 Å2
MethodPISA
4
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

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)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
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_556-y,x-y,z+11
crystal symmetry operation3_556-x+y,-x,z+11
Buried area13980 Å2
ΔGint-206 kcal/mol
Surface area19380 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 FOLLOWING RESIDUES ARE DISORDERED - VAL B 12, GLU B 21, ARG B 22, THR B 27, ARG D 22, LYS D 29.
2: DISORDER IN RESIDUE VAL B 12 PRECLUDES USE OF STANDARD NOMENCLATURE FOR HYDROGEN ATOMS IN THIS RESIDUE. THE HYDROGEN ATOMS, THEREFORE, ARE ARBITRARILY NAMED. ALSO SEE FTNOTE 1.
Components on special symmetry positions
IDModelComponents
11B-31-

ZN

21D-31-

ZN

31D-40-

DOD

41D-83-

DOD

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 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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: D2O
Has protein modificationY

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Experimental details

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Experiment

Experiment
Method
X-RAY DIFFRACTION
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36.05 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %d6-acetone11
270 %11D2O
30.1 Msodium citrate11
40.005 %zinc chloride11

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Data collection

Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 10 Å / Observed criterion σ(F): 0 / Num. measured all: 13476

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Processing

SoftwareName: PROLSQ / Classification: refinement
Refinement
Refine-IDRfactor RworkHighest resolution (Å)Diffraction-ID
X-RAY DIFFRACTION0.1821.51
NEUTRON DIFFRACTION2.22
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 2 325 1133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.019
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_deg
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: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS

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