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- PDB-3v1g: Forestalling insulin fibrillation by insertion of a chiral clamp ... -

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Basic information

Entry
Database: PDB / ID: 3v1g
TitleForestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health
Components(Insulin) x 2
KeywordsHORMONE / zinc-binding site / long-acting insulin analog / receptor binding protein engineering / insulin fibrillation
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 / Signal attenuation / positive regulation of nitric oxide mediated signal transduction / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / negative regulation of lipid catabolic process / fatty acid homeostasis / endosome lumen / positive regulation of insulin receptor signaling pathway / Regulation of insulin secretion / endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / negative regulation of gene expression / endoplasmic reticulum lumen / 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 / insulin-like growth factor / relaxin family. / Insulin/IGF/Relaxin family / Insulin-like / Insulin family signature. / Insulin-like superfamily / Insulin, conserved site
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWan, Z.L. / Hua, Q.X. / Wickramasinghe, N.P. / Huang, K. / Petkova, A.T. / Hu, S.Q. / Phillips, N.B. / Yeh, I.J. / Whittake, J. / Ismail-Beigi, F. ...Wan, Z.L. / Hua, Q.X. / Wickramasinghe, N.P. / Huang, K. / Petkova, A.T. / Hu, S.Q. / Phillips, N.B. / Yeh, I.J. / Whittake, J. / Ismail-Beigi, F. / Katsoyyannis, P.G. / Tycko, R. / Weiss, M.A.
Citation
Journal: To be Published
Title: Forestalling insulin fibrillation by insertion of a chiral clamp mechanism-based application of protein engineering to global health
Authors: Wan, Z.L. / Hua, Q.X. / Wickramasinghe, N.P. / Huang, K. / Petkova, A.T. / Hu, S.Q. / Phillips, N.B. / Yeh, I.J. / Whittake, J. / Ismail-Beigi, F. / Katsoyyannis, P.G. / Tycko, R. / Weiss, M.A.
#1: Journal: Biochemistry / Year: 2005
Title: Diabetes-associated mutations in human insulin: crystal structure and photo-cross-linking studies of a-chain variant insulin Wakayama
Authors: Wan, Z.L. / Huang, K. / Xu, B. / Hu, S.Q. / Wang, S. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
#2: Journal: Biochemistry / Year: 2003
Title: Crystal structure of allo-Ile(A2)-insulin, an inactive chiral analogue: implications for the mechanism of receptor binding
Authors: Wan, Z.L. / Xu, B. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A.
#3: Journal: Biochemistry / Year: 2004
Title: Enhancing the activity of insulin at the receptor interface: crystal structure and photo-cross-linking of A8 analogues
Authors: L Wan, Z. / Xu, B. / Chu, Y.C. / Li, B. / Nakagawa, S.H. / Qu, Y. / Hu, S.Q. / Katsoyannis, P.G. / Weiss, M.A.
#5: Journal: Nature / Year: 1976
Title: Structure of insulin in 4-zinc insulin
Authors: Bentley, G. / Dodson, E. / Dodson, G. / Hodgkin, D. / Mercola, D.
#6: Journal: Nature / Year: 1989
Title: Phenol stabilizes more helix in a new symmetrical zinc insulin hexamer
Authors: Derewenda, U. / Derewenda, Z. / Dodson, E. / Dodson, G. / Reynold, C. / Smith, G. / Sparks, C. / Swenson, D.
History
DepositionDec 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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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)11,8968
Polymers11,6354
Non-polymers2604
Water1,45981
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)35,68724
Polymers34,90612
Non-polymers78112
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area19020 Å2
ΔGint-294 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.081, 79.081, 37.402
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-31-

ZN

21D-31-

ZN

31D-32-

CL

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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: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#2: Protein/peptide Insulin /


Mass: 3433.953 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308

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Non-polymers , 4 types, 85 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IPH / PHENOL / Phenol


Mass: 94.111 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6O
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 81 / 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: 1.93 Å3/Da / Density % sol: 36.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: 0.02 M Tris, 0.05 M sodium citrate, 5% acetone, 0.03% phenol, 0.01% zinc acetate, pH 8.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: Bruker AXIOM 200 / Detector: CCD / Date: Jan 14, 2005 / Details: Optics Mirrors
RadiationMonochromator: Monochromator Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→39.54 Å / Num. all: 4417 / Num. obs: 4321 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 16.9
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.7 / Num. unique all: 632 / % possible all: 100

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Processing

Software
NameClassification
PROTEUM PLUSdata collection
CNSrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TRZ
Resolution: 2.2→39.54 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.323 448 -Random
Rwork0.229 ---
all-4417 --
obs-4212 95.3 %-
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.06 Å20 Å20 Å2
2---4.06 Å20 Å2
3---8.13 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 2.2→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms810 0 10 81 901
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_improper_angle_d5.41
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.052
RfactorNum. reflection% reflection
Rfree0.391 56 -
Rwork0.251 --
obs-632 93.9 %

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