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- PDB-3mth: X-RAY CRYSTALLOGRAPHIC STUDIES ON HEXAMERIC INSULINS IN THE PRESE... -

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Entry
Database: PDB / ID: 3mth
TitleX-RAY CRYSTALLOGRAPHIC STUDIES ON HEXAMERIC INSULINS IN THE PRESENCE OF HELIX-STABILIZING AGENTS, THIOCYANATE, METHYLPARABEN AND PHENOL
Components(METHYLPARABEN ...) x 2
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 D-glucose import / positive regulation of protein secretion / 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
4-HYDROXY-BENZOIC ACID METHYL ESTER / Insulin
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWhittingham, J.L. / Dodson, E.J. / Moody, P.C.E. / Dodson, G.G.
Citation
Journal: Biochemistry / Year: 1995
Title: X-ray crystallographic studies on hexameric insulins in the presence of helix-stabilizing agents, thiocyanate, methylparaben, and phenol.
Authors: Whittingham, J.L. / Chaudhuri, S. / Dodson, E.J. / Moody, P.C. / Dodson, G.G.
#1: Journal: Biopolymers / Year: 1992
Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol
Authors: Smith, G.D. / Dodson, G.G.
#2: 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.
History
DepositionSep 13, 1995Processing site: BNL
SupersessionJan 29, 1996ID: 2MTH
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: 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 / 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_database_status.process_site / _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 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9299
Polymers11,5754
Non-polymers3545
Water1,35175
1
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0415
Polymers5,7882
Non-polymers2533
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-11 kcal/mol
Surface area3910 Å2
MethodPISA
2
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8884
Polymers5,7882
Non-polymers1012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-14 kcal/mol
Surface area3700 Å2
MethodPISA
3
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,78727
Polymers34,72612
Non-polymers1,06215
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 area19870 Å2
ΔGint-315 kcal/mol
Surface area11830 Å2
MethodPISA
4
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules

C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9299
Polymers11,5754
Non-polymers3545
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4060 Å2
ΔGint-33 kcal/mol
Surface area6360 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-34 kcal/mol
Surface area5940 Å2
MethodPISA
6
C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules

C: METHYLPARABEN INSULIN
D: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,66512
Polymers17,3636
Non-polymers3036
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 area6080 Å2
ΔGint-123 kcal/mol
Surface area10540 Å2
MethodPISA
7
A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules

A: METHYLPARABEN INSULIN
B: METHYLPARABEN INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,12215
Polymers17,3636
Non-polymers7599
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 area5080 Å2
ΔGint-145 kcal/mol
Surface area10010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.380, 80.380, 37.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-31-

ZN

21B-32-

CL

31D-31-

ZN

41D-32-

CL

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Components

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METHYLPARABEN ... , 2 types, 4 molecules ACBD

#1: Protein/peptide METHYLPARABEN INSULIN


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315
#2: Protein/peptide METHYLPARABEN INSULIN


Mass: 3403.927 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P01315

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Non-polymers , 4 types, 80 molecules

#3: Chemical ChemComp-MPB / 4-HYDROXY-BENZOIC ACID METHYL ESTER


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.99 Å3/Da / Density % sol: 38.09 %
Crystal grow
*PLUS
pH: 8 / Method: batch method
Components of the solutions
*PLUS
Conc.: 0.02 M / Common name: hydrochrolic acid

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 5.95 Å / Num. obs: 6095 / % possible obs: 86.3 % / Num. measured all: 6620 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 28.1 % / Mean I/σ(I) obs: 4.32

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.1843 6095
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms789 0 15 75 879
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2163
X-RAY DIFFRACTIONp_mcangle_it3.8013.5
X-RAY DIFFRACTIONp_scbond_it2.4763
X-RAY DIFFRACTIONp_scangle_it3.9453.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.0780.1
X-RAY DIFFRACTIONp_singtor_nbd0.1640.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.20820
X-RAY DIFFRACTIONp_staggered_tor22.54520
X-RAY DIFFRACTIONp_orthonormal_tor15.11420
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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