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- PDB-1zeg: STRUCTURE OF B28 ASP INSULIN IN COMPLEX WITH PHENOL -

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Entry
Database: PDB / ID: 1zeg
TitleSTRUCTURE OF B28 ASP INSULIN IN COMPLEX WITH PHENOL
Components(INSULIN) x 2
KeywordsHORMONE / METABOLIC ROLE / CHEMICAL ACTIVITY / INSULIN MUTANT / CROSS-LINK / GLUCOSE METABOLISM / DIABETES
Function / homology
Function and homology information


negative regulation of glycogen catabolic process / Signaling by Insulin receptor / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / nitric oxide-cGMP-mediated signaling pathway / Insulin receptor recycling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...negative regulation of glycogen catabolic process / Signaling by Insulin receptor / regulation of cellular amino acid metabolic process / IRS activation / negative regulation of NAD(P)H oxidase activity / Insulin processing / nitric oxide-cGMP-mediated signaling pathway / Insulin receptor recycling / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Regulation of gene expression in beta cells / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of respiratory burst involved in inflammatory response / alpha-beta T cell activation / negative regulation of gluconeogenesis / negative regulation of acute inflammatory response / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of dendritic spine maintenance / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of glycogen biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of protein secretion / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / Signal attenuation / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / positive regulation of insulin receptor signaling pathway / endoplasmic reticulum-Golgi intermediate compartment membrane / Regulation of insulin secretion / transport vesicle / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of brown fat cell differentiation / positive regulation of mitotic nuclear division / positive regulation of long-term synaptic potentiation / regulation of transmembrane transporter activity / positive regulation of cell differentiation / regulation of synaptic plasticity / activation of protein kinase B activity / cognition / positive regulation of cytokine production / positive regulation of protein secretion / acute-phase response / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of nitric-oxide synthase activity / hormone activity / insulin receptor binding / vasodilation / negative regulation of protein catabolic process / insulin receptor signaling pathway / positive regulation of protein localization to nucleus / wound healing / Golgi lumen / regulation of protein localization / glucose metabolic process / glucose homeostasis / cell-cell signaling / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / positive regulation of NF-kappaB transcription factor activity / positive regulation of protein kinase B signaling / positive regulation of MAPK cascade / protease binding / G protein-coupled receptor signaling pathway / positive regulation of cell migration / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin family signature. / Insulin, conserved site / Insulin-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsWhittingham, J.L. / Edwards, E.J. / Antson, A.A. / Clarkson, J.M. / Dodson, G.G.
Citation
Journal: Biochemistry / Year: 1998
Title: Interactions of phenol and m-cresol in the insulin hexamer, and their effect on the association properties of B28 pro --> Asp insulin analogues.
Authors: Whittingham, J.L. / Edwards, D.J. / Antson, A.A. / Clarkson, J.M. / Dodson, G.G.
#1: Journal: Structure / Year: 1995
Title: Role of C-Terminal B-Chain Residues in Insulin Assembly: The Structure of Hexameric Lysb28Prob29-Human Insulin
Authors: Ciszak, E. / Beals, J.M. / Frank, B.H. / Baker, J.C. / Carter, N.D. / Smith, G.D.
#2: Journal: Biopolymers / Year: 1992
Title: The Structure of a Rhombohedral R6 Insulin Hexamer that Binds Phenol
Authors: Smith, G.D. / Dodson, G.G.
History
DepositionMay 1, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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
B: INSULIN
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,15511
Polymers11,6714
Non-polymers4847
Water1,946108
1
A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1256
Polymers5,8362
Non-polymers2894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-13 kcal/mol
Surface area4330 Å2
MethodPISA
2
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0315
Polymers5,8362
Non-polymers1953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-12 kcal/mol
Surface area4190 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)36,46633
Polymers35,01412
Non-polymers1,45221
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 area21440 Å2
ΔGint-317 kcal/mol
Surface area12100 Å2
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-26 kcal/mol
Surface area6690 Å2
MethodPISA
5
C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
B: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,15511
Polymers11,6714
Non-polymers4847
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area3580 Å2
ΔGint-25 kcal/mol
Surface area7450 Å2
MethodPISA
6
A: INSULIN
C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
C: INSULIN
D: INSULIN
hetero molecules

A: INSULIN
C: INSULIN
D: INSULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,52521
Polymers24,6589
Non-polymers86712
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 area7880 Å2
ΔGint-150 kcal/mol
Surface area15350 Å2
MethodPISA
7
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)25,80824
Polymers24,6589
Non-polymers1,15015
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 area7360 Å2
ΔGint-162 kcal/mol
Surface area15470 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)18,37418
Polymers17,5076
Non-polymers86712
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 area5980 Å2
ΔGint-160 kcal/mol
Surface area10730 Å2
MethodPISA
9
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)18,09215
Polymers17,5076
Non-polymers5859
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 area6820 Å2
ΔGint-149 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.730, 77.730, 39.160
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

51B-34-

HOH

61D-33-

HOH

71D-34-

HOH

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide INSULIN / / B28ASP-PHN


Mass: 2383.698 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, P28D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P01308
#2: Protein/peptide INSULIN / / B28ASP-PHN


Mass: 3451.926 Da / Num. of mol.: 2 / Mutation: CHAIN B, D, P28D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P01308

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Non-polymers , 4 types, 115 molecules

#3: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6O
#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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 40 %
Crystal growMethod: batch method / pH: 6.5
Details: BATCH METHOD, COMPOSITION OF CRYSTALLISATION SOLUTION 3.5 MG INSULIN + 0.5 ML 0.02M HCL + 0.05 ML 0.12M ZINC ACETATE + 0.25 ML 0.2M TRI-SODIUM CITRATE + 0.2 ML 2.5% (W/V) PHENOL IN ETHANOL + ...Details: BATCH METHOD, COMPOSITION OF CRYSTALLISATION SOLUTION 3.5 MG INSULIN + 0.5 ML 0.02M HCL + 0.05 ML 0.12M ZINC ACETATE + 0.25 ML 0.2M TRI-SODIUM CITRATE + 0.2 ML 2.5% (W/V) PHENOL IN ETHANOL + 60 MG NACL, pH 6.5, batch method
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 50 ℃ / Method: batch method / PH range low: 6.8 / PH range high: 6.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
20.02 M110.500mlHCl
30.12 Mzinc acetate110.050ml
40.2 Mtrisodium citrate110.250ml
52.5 %phenol in ethanol110.200ml
1insulin113.5mg
61160mgNaCl

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→14.7 Å / Num. obs: 11469 / % possible obs: 98.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.023
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.038 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 74966
Reflection shell
*PLUS
% possible obs: 97.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementStarting model: B28ASP INSULIN WITH M-CRESOL DIMER

Resolution: 1.6→14.7 Å / Cross valid method: FREE R / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.192 -5 %5
Rwork0.145 ---
obs-11469 98.9 %-
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.6→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 25 106 943
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5892
X-RAY DIFFRACTIONp_mcangle_it2.3633
X-RAY DIFFRACTIONp_scbond_it2.3142
X-RAY DIFFRACTIONp_scangle_it3.4023
X-RAY DIFFRACTIONp_plane_restr0.0270.03
X-RAY DIFFRACTIONp_chiral_restr0.0840.1
X-RAY DIFFRACTIONp_singtor_nbd0.1650.3
X-RAY DIFFRACTIONp_multtor_nbd0.2780.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1340.3
X-RAY DIFFRACTIONp_planar_tor5.77
X-RAY DIFFRACTIONp_staggered_tor11.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor15.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 11469 / Rfactor all: 0.145
Solvent computation
*PLUS
Displacement parameters
*PLUS

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