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- PDB-3hyd: LVEALYL peptide derived from human insulin chain B, residues 11-17 -

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Basic information

Entry
Database: PDB / ID: 3hyd
TitleLVEALYL peptide derived from human insulin chain B, residues 11-17
ComponentsInsulin
KeywordsPROTEIN FIBRIL / amyloid-like protofibril / Carbohydrate metabolism / Cleavage on pair of basic residues / Diabetes mellitus / Disease mutation / Disulfide bond / Glucose metabolism / Hormone / Pharmaceutical / Secreted
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 / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsIvanova, M.I. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Molecular basis for insulin fibril assembly.
Authors: Ivanova, M.I. / Sievers, S.A. / Sawaya, M.R. / Wall, J.S. / Eisenberg, D.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin


Theoretical massNumber of molelcules
Total (without water)8201
Polymers8201
Non-polymers00
Water543
1
A: Insulin

A: Insulin

A: Insulin

A: Insulin


Theoretical massNumber of molelcules
Total (without water)3,2804
Polymers3,2804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
crystal symmetry operation4_566-x+1/2,y+3/2,-z+11
Unit cell
Length a, b, c (Å)49.478, 4.838, 19.442
Angle α, β, γ (deg.)90.000, 96.650, 90.000
Int Tables number5
Space group name H-MC121
DetailsTHE BIOLOGICAL UNIT IS A INDEFINITELY LONG PAIR OF SHEETS (A PROTOFIBRIL). ONE SHEET FORMED BY CHAIN A AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE B CELL DIMENSION (E.G. X,Y,Z AND X,Y+1,Z). THE SECOND SHEET IS CONSTRUCTED FROM 1/2-X,1/2+Y,1-Z AND CRYSTALLOGRAPHIC TRANSLATIONS ALONG THE B CELL DIMENSION (E.G. 1/2-X,3/2+Y,1-Z).

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Components

#1: Protein/peptide Insulin / / Insulin B chain


Mass: 819.985 Da / Num. of mol.: 1 / Fragment: UNP residues 34-41 of chain B / Source method: obtained synthetically / References: UniProt: P01308
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% MPD, 0.1M sodium citrate pH 5.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X10SA10.97645
SYNCHROTRONSLS X10SA20.97645
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDNov 19, 2006
MARMOSAIC 225 mm CCD2CCDNov 19, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.97645 Å / Relative weight: 1
ReflectionResolution: 1→90 Å / Num. all: 2647 / Num. obs: 2647 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 6.6 Å2 / Rmerge(I) obs: 0.184 / Χ2: 1.034 / Net I/σ(I): 7.152
Reflection shellResolution: 1→1.08 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 3.26 / Num. unique all: 433 / Χ2: 1.042 / % possible all: 84.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å19.33 Å
Translation1.6 Å19.33 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: an idealized beta strand

Resolution: 1→16.14 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.196 / WRfactor Rwork: 0.158 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.878 / SU B: 0.849 / SU ML: 0.019 / SU R Cruickshank DPI: 0.03 / SU Rfree: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18 248 9.4 %RANDOM
Rwork0.146 ---
all0.149 ---
obs0.149 2644 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 29.45 Å2 / Biso mean: 6.558 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0.28 Å2
2---0.55 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1→16.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms133 0 0 3 136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02365
X-RAY DIFFRACTIONr_bond_other_d0.0050.0269
X-RAY DIFFRACTIONr_angle_refined_deg1.792.12290
X-RAY DIFFRACTIONr_angle_other_deg0.8513158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.5726.6673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.0591512
X-RAY DIFFRACTIONr_chiral_restr0.1470.212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0269
X-RAY DIFFRACTIONr_gen_planes_other00.0211
X-RAY DIFFRACTIONr_mcbond_it2.258238
X-RAY DIFFRACTIONr_mcbond_other0.821217
X-RAY DIFFRACTIONr_mcangle_it3.043361
X-RAY DIFFRACTIONr_scbond_it3.713227
X-RAY DIFFRACTIONr_scangle_it5.334328
X-RAY DIFFRACTIONr_rigid_bond_restr2.4693134
X-RAY DIFFRACTIONr_sphericity_free15.40733
X-RAY DIFFRACTIONr_sphericity_bonded3.7083133
LS refinement shellResolution: 1→1.118 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.338 68 -
Rwork0.232 583 -
all-651 -
obs--88.45 %

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