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- PDB-1ev3: Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer -

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Basic information

Entry
Database: PDB / ID: 1ev3
TitleStructure of the rhombohedral form of the M-cresol/insulin R6 hexamer
Components(INSULIN) x 2
KeywordsHORMONE/GROWTH FACTOR / R6 Hexamer / 18-A / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior ...Signaling by Insulin receptor / alpha-beta T cell activation / negative regulation of glycogen catabolic process / Insulin processing / IRS activation / Insulin receptor recycling / negative regulation of NAD(P)H oxidase activity / nitric oxide-cGMP-mediated signaling pathway / 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 / negative regulation of gluconeogenesis / positive regulation of cellular protein metabolic process / negative regulation of reactive oxygen species biosynthetic process / COPI-mediated anterograde transport / regulation of cellular amino acid metabolic process / regulation of protein localization to plasma membrane / Regulation of insulin secretion / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Signal attenuation / negative regulation of protein secretion / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / transport vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of insulin receptor signaling pathway / neuron projection maintenance / insulin-like growth factor receptor binding / positive regulation of protein autophosphorylation / positive regulation of glycolytic process / negative regulation of acute inflammatory response / positive regulation of cell differentiation / regulation of transmembrane transporter activity / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / regulation of synaptic plasticity / positive regulation of brown fat cell differentiation / cognition / regulation of protein localization / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / acute-phase response / activation of protein kinase B activity / positive regulation of glucose import / vasodilation / hormone activity / negative regulation of proteolysis / negative regulation of protein catabolic process / insulin receptor binding / positive regulation of protein localization to nucleus / insulin receptor signaling pathway / glucose metabolic process / Golgi lumen / positive regulation of nitric-oxide synthase activity / cell-cell signaling / glucose homeostasis / endoplasmic reticulum to Golgi vesicle-mediated transport / wound healing / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell migration / positive regulation of protein kinase B signaling / Golgi membrane / Amyloid fiber formation / G protein-coupled receptor signaling pathway / amyloid fibril formation / endoplasmic reticulum lumen / regulation of transcription, DNA-templated / positive regulation of gene expression / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / Resolution: 1.78 Å
AuthorsSmith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: R6 hexameric insulin complexed with m-cresol or resorcinol.
Authors: Smith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H.
#1: Journal: Proteins / Year: 1992
Title: Structure of a Rhombohedral R6 Insulin/Phenol Complex
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
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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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)12,16111
Polymers11,6354
Non-polymers5267
Water1,58588
1
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)36,48433
Polymers34,90612
Non-polymers1,57821
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 area20660 Å2
ΔGint-308 kcal/mol
Surface area11140 Å2
MethodPISA, PQS
Unit cell
γ
α
β
Length a, b, c (Å)78.866, 78.866, 39.465
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-33-

HOH

61D-33-

HOH

71D-55-

HOH

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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 / Fragment: RESIDUES 87-107 / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (human)
References: UniProt: P01308
#2: Protein/peptide INSULIN /


Mass: 3433.953 Da / Num. of mol.: 2 / Fragment: RESIDUES 25-54 / Source method: obtained synthetically
Details: This sequence occurs naturally in homo sapiens (human)
References: UniProt: P01308

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Non-polymers , 4 types, 95 molecules

#3: Chemical ChemComp-CRS / M-CRESOL / M-Cresol


Mass: 108.138 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8O
#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.: 88 / 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: 2.03 Å3/Da / Density % sol: 39.41 %
Crystal growTemperature: 298 K / Method: slow cooling / pH: 8.5
Details: 30 mg insulin, 3.0 ml of 0.02 M HCl, 0.3 ml of 0.15 M Zinc Acetate, 1.5 ml of 0.2 M Sodium Citrate, 1.2 ml of 2.5% m-cresol in acetone, 0.36 gm sodium chloride, pH 8.5, SLOW COOLING, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
20.02 M113.0mlHCl
30.15 Mzinc acetate110.3ml
40.2 Msodium citrate111.5ml
52.5 %m-cresol in acetone111.2ml
1insulin1130mg
6110.36gNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 13, 2000 / Details: OSMIC CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→19.72 Å / Num. all: 9334 / Num. obs: 9334 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 60.6
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 10 / % possible all: 82.6
Reflection
*PLUS
Num. measured all: 64359
Reflection shell
*PLUS
% possible obs: 82.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
CNS1phasing
RefinementResolution: 1.78→19.72 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 885 10.3 %Random
Rwork0.2 ---
all0.2 8552 --
obs0.2 8552 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.69 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20.73 Å20 Å2
2---0.96 Å20 Å2
3---1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.78→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms755 0 28 88 871
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d20.3
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.782
X-RAY DIFFRACTIONc_mcangle_it2.722.5
X-RAY DIFFRACTIONc_scbond_it2.362.5
X-RAY DIFFRACTIONc_scangle_it3.413
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.32 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 136 10.4 %
Rwork0.336 1173 -
obs--88.2 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.3 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it2.5
X-RAY DIFFRACTIONc_mcangle_it2.5
X-RAY DIFFRACTIONc_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.371 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.336 / Rfactor obs: 0.336

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