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- PDB-1mso: T6 Human Insulin at 1.0 A Resolution -

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Basic information

Entry
Database: PDB / ID: 1mso
TitleT6 Human Insulin at 1.0 A Resolution
Components
  • Insulin A-Chain
  • Insulin B-Chain
KeywordsHORMONE/GROWTH FACTOR / T6 Conformation / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / cognition / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / 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 / 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, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsSmith, G.D. / Pangborn, W.A. / Blessing, R.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: The structure of T6 human insulin at 1.0 A resolution.
Authors: Smith, G.D. / Pangborn, W.A. / Blessing, R.H.
History
DepositionSep 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin A-Chain
B: Insulin B-Chain
C: Insulin A-Chain
D: Insulin B-Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7666
Polymers11,6354
Non-polymers1312
Water4,071226
1
A: Insulin A-Chain
B: Insulin B-Chain
C: Insulin A-Chain
D: Insulin B-Chain
hetero molecules

A: Insulin A-Chain
B: Insulin B-Chain
C: Insulin A-Chain
D: Insulin B-Chain
hetero molecules

A: Insulin A-Chain
B: Insulin B-Chain
C: Insulin A-Chain
D: Insulin B-Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,29818
Polymers34,90612
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 area19340 Å2
ΔGint-249 kcal/mol
Surface area12750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)81.286, 81.286, 33.714
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Cell settingtrigonal
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11D-501-

ZN

21D-502-

ZN

31B-606-

HOH

41B-634-

HOH

DetailsThe insulin hexamer is generated from the dimer in the asymmetry unit by the symmetry operations, x,y,z; -y,x-y,z; y-x,-x,z

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Components

#1: Protein/peptide Insulin A-Chain


Mass: 2383.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in Homo Sapiens / References: UniProt: P01308
#2: Protein/peptide Insulin B-Chain


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This sequence occurs naturally in Homo Sapiens / References: UniProt: P01308
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.84 Å3/Da / Density % sol: 33.22 %
Crystal growTemperature: 298 K / Method: slow cooling / pH: 6.3
Details: 0.001 M HCl, 0.007 M Zinc Acetate, 0.05 M Sodium Citrate, 17% acetone, pH 6.3, SLOW COOLING at 298K, temperature 298.0K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlinsulin11
20.01 M11HCl
30.007 Mzinc acetate11
40.05 Msodium citrate11
517 %acetone11pH6.3

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 2000 / Detector: CCD / Date: Nov 1, 1997
RadiationMonochromator: Gobel diffraction-mirrors monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1→30.4 Å / Num. all: 41170 / Num. obs: 41170 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 7.42 Å2 / Rmerge(I) obs: 0.0491 / Net I/σ(I): 11
Reflection shellResolution: 1→1.02 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.3 / % possible all: 75
Reflection
*PLUS
Num. measured all: 72631

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Processing

Software
NameVersionClassification
sortavdata reduction
CNS1.1refinement
SMARTV. 2000 (BRUKER)data reduction
SORTAVdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4ins

4ins


Resolution: 1→30.4 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used CNS_Solve Version 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4194 10.2 %Random
Rwork0.183 ---
all0.183 41170 --
obs0.183 41170 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.93 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso mean: 12.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.54 Å20 Å2
2--0.89 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.14 Å0.12 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 2 226 1032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.9282
X-RAY DIFFRACTIONc_mcangle_it2.3872.5
X-RAY DIFFRACTIONc_scbond_it3.8422.5
X-RAY DIFFRACTIONc_scangle_it3.8923
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d1.1
LS refinement shellResolution: 1→1.06 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 556 9.6 %
Rwork0.382 5238 -
obs--77.6 %
Refinement
*PLUS
Highest resolution: 1 Å / Num. reflection obs: 41242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1
X-RAY DIFFRACTIONc_mcbond_it1.93
X-RAY DIFFRACTIONc_scbond_it3.84
X-RAY DIFFRACTIONc_mcangle_it2.39
X-RAY DIFFRACTIONc_scangle_it3.89

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