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- PDB-1tyl: THE STRUCTURE OF A COMPLEX OF HEXAMERIC INSULIN AND 4'-HYDROXYACE... -

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Entry
Database: PDB / ID: 1tyl
TitleTHE STRUCTURE OF A COMPLEX OF HEXAMERIC INSULIN AND 4'-HYDROXYACETANILIDE
Components(INSULIN) x 2
KeywordsHORMONE
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / 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 / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / 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 / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / positive regulation of protein autophosphorylation / Insulin receptor recycling / transport vesicle / insulin-like growth factor receptor binding / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / positive regulation of protein metabolic process / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / endosome lumen / Regulation of insulin secretion / positive regulation of D-glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / positive regulation of neuron projection development / cognition / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / glucose homeostasis / regulation of protein localization / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / extracellular space / extracellular region / 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
N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL) / Insulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSmith, G.D. / Ciszak, E.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: The structure of a complex of hexameric insulin and 4'-hydroxyacetanilide.
Authors: Smith, G.D. / Ciszak, E.
#1: Journal: Biochemistry / Year: 1994
Title: Crystallographic Evidence for Dual Coordination Around Zinc in the T3R3 Human Insulin Hexamer
Authors: Ciszak, E. / Smith, G.D.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1984
Title: Structural Stability in the 4-Zinc Human Insulin Hexamer
Authors: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D.
History
DepositionJun 21, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,9538
Polymers11,6354
Non-polymers3174
Water1,982110
1
A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8833
Polymers5,8182
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-15 kcal/mol
Surface area3630 Å2
MethodPISA
2
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0705
Polymers5,8182
Non-polymers2523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-11 kcal/mol
Surface area3720 Å2
MethodPISA
3
A: INSULIN
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)35,85824
Polymers34,90612
Non-polymers95212
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 area18930 Å2
ΔGint-281 kcal/mol
Surface area11960 Å2
MethodPISA
4
C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9538
Polymers11,6354
Non-polymers3174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4020 Å2
ΔGint-32 kcal/mol
Surface area6170 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-35 kcal/mol
Surface area5800 Å2
MethodPISA
6
A: INSULIN
B: INSULIN
C: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
C: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,25415
Polymers24,6049
Non-polymers6506
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 area7160 Å2
ΔGint-102 kcal/mol
Surface area15010 Å2
MethodPISA
7
C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules

C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,20915
Polymers17,4536
Non-polymers7569
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 area5010 Å2
ΔGint-139 kcal/mol
Surface area9710 Å2
MethodPISA
8
A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6499
Polymers17,4536
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 area5750 Å2
ΔGint-94 kcal/mol
Surface area10420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.110, 81.110, 37.970
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

21D-31-

ZN

31D-32-

CL

41B-32-

HOH

51D-52-

HOH

61D-53-

HOH

DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT OF INSULIN CONSISTS OF TWO INSULIN MONOMERS EACH CONSISTING OF TWO HETEROCHAINS. THE ENTRY PRESENTS COORDINATES FOR MONOMER I (CHAIN IDENTIFIERS A AND B) AND II (CHAIN IDENTIFIERS C AND D). APPLYING THE THREE-FOLD CRYSTALLOGRAPHIC SYMMETRY AXIS YIELDS A HEXAMER AROUND THE AXIS. THERE ARE TWO ZINC IONS PER INSULIN HEXAMER LOCATED ON THE THREE-FOLD AXIS. WATERS HOH 1, HOH 104, AND HOH 105 ARE LOCATED ON THE THREE-FOLD AXIS.

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide INSULIN


Mass: 2383.698 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide INSULIN


Mass: 3433.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 114 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-TYL / N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL)


Mass: 151.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9NO2 / Comment: medication*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE CONFORMATIONS OF THE TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A DIFFERENCE IN CONFORMATION ...THE CONFORMATIONS OF THE TWO MONOMERS ARE DIFFERENT AS THE RESULT OF A DIFFERENCE IN CONFORMATION AT THE N-TERMINI OF THE B AND D CHAINS. IN MONOMER I, B 1 - B 8 ADOPT AN EXTENDED CONFORMATION (T STATE) WHILE IN MONOMER II RESIDUES D 4 THROUGH D 8 ARE ALPHA-HELICAL (R STATE).
Nonpolymer detailsEACH OF TWO ZINC IONS IS COORDINATED BY THE THREE SYMMETRY RELATED HIS B 10 SIDE CHAINS. THE ...EACH OF TWO ZINC IONS IS COORDINATED BY THE THREE SYMMETRY RELATED HIS B 10 SIDE CHAINS. THE COORDINATION SPHERE OF ZN B 1 IS OCTAHEDRAL WITH THE REMAINING THREE SITES FILLED BY WATER, HOH 16. THE COORDINATION OF ZN D 1 IS TETRAHEDRAL TO CL D 2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal grow
*PLUS
Temperature: 290 K / pH: 6.4 / Method: unknown
Components of the solutions
*PLUS
IDUnitCommon nameCrystal-IDSol-IDChemical formula
1MTylenol11
3Msodium citrate11
4Mzinc acetate11
5M4'-hydroxyacetanilide11
6Msodium chloride11
2M11NaCl

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 9999 Å / Num. obs: 6783 / Observed criterion σ(F): 2 / Num. measured all: 28940 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 46 %

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Processing

SoftwareName: PROFFT / Classification: refinement
RefinementRfactor obs: 0.168 / Highest resolution: 1.9 Å
Refinement stepCycle: LAST / Highest resolution: 1.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 14 110 915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection all: 6687 / Num. reflection obs: 6316 / σ(F): 2 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.040.047
X-RAY DIFFRACTIONp_planar_d0.050.049
X-RAY DIFFRACTIONp_plane_restr0.020.013
X-RAY DIFFRACTIONp_chiral_restr0.150.174

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