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- PDB-2omq: VEALYL peptide derived from human insulin chain B, residues 12-17 -

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Basic information

Entry
Database: PDB / ID: 2omq
TitleVEALYL peptide derived from human insulin chain B, residues 12-17
ComponentsVEALYL peptide derived from human insulin chain B, residues 12-17
KeywordsPROTEIN FIBRIL / steric zipper / anti-parallel beta-sheet
Function / homology
Function and homology information


negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / positive regulation of protein autophosphorylation / alpha-beta T cell activation / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / Signal attenuation / fatty acid homeostasis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of insulin receptor signaling pathway / negative regulation of lipid catabolic process / regulation of protein localization to plasma membrane / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / activation of protein kinase B activity / COPI-mediated anterograde transport / transport vesicle / nitric oxide-cGMP-mediated signaling / negative regulation of reactive oxygen species biosynthetic process / Insulin receptor recycling / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of nitric-oxide synthase activity / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / regulation of transmembrane transporter activity / positive regulation of glycolytic process / positive regulation of long-term synaptic potentiation / positive regulation of cytokine production / endosome lumen / acute-phase response / positive regulation of D-glucose import / positive regulation of protein secretion / positive regulation of cell differentiation / Regulation of insulin secretion / insulin receptor binding / wound healing / negative regulation of protein catabolic process / hormone activity / regulation of synaptic plasticity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / cognition / glucose metabolic process / vasodilation / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / positive regulation of cell growth / secretory granule lumen / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / 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-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIvanova, M. / Sawaya, M.R. / Eisenberg, D.
CitationJournal: Nature / Year: 2007
Title: Atomic structures of amyloid cross-beta spines reveal varied steric zippers.
Authors: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A. / Riekel, C. / Eisenberg, D.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 25, 2014Group: Other
Revision 1.4Apr 22, 2015Group: Structure summary
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software
Revision 1.6Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: VEALYL peptide derived from human insulin chain B, residues 12-17
B: VEALYL peptide derived from human insulin chain B, residues 12-17
C: VEALYL peptide derived from human insulin chain B, residues 12-17
D: VEALYL peptide derived from human insulin chain B, residues 12-17


Theoretical massNumber of molelcules
Total (without water)2,8274
Polymers2,8274
Non-polymers00
Water724
1
A: VEALYL peptide derived from human insulin chain B, residues 12-17
B: VEALYL peptide derived from human insulin chain B, residues 12-17
C: VEALYL peptide derived from human insulin chain B, residues 12-17
D: VEALYL peptide derived from human insulin chain B, residues 12-17

A: VEALYL peptide derived from human insulin chain B, residues 12-17
B: VEALYL peptide derived from human insulin chain B, residues 12-17
C: VEALYL peptide derived from human insulin chain B, residues 12-17
D: VEALYL peptide derived from human insulin chain B, residues 12-17


Theoretical massNumber of molelcules
Total (without water)5,6558
Polymers5,6558
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Unit cell
Length a, b, c (Å)18.425, 9.613, 21.975
Angle α, β, γ (deg.)90.880, 96.120, 100.930
Int Tables number1
Space group name H-MP1
DetailsA steric zipper can be generated by repeated unit cell translations of the asymmetric unit along the b axis.

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Components

#1: Protein/peptide
VEALYL peptide derived from human insulin chain B, residues 12-17


Mass: 706.827 Da / Num. of mol.: 4 / Fragment: residues 12-17 / Source method: obtained synthetically / References: UniProt: P01308*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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

Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 2.5
Details: 2mM peptide in 100 mM NaCl and 50 mM phosphate. Crystals can be more easily reproduced by dissolving peptide to 2 mM in water at room temperature, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.9466
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9466 Å / Relative weight: 1
ReflectionResolution: 1.7→90 Å / Num. obs: 820 / % possible obs: 93 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.065 / Net I/σ(I): 3.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.830.4132991.071191.7
1.83-2.020.322961.094188.6
2.02-2.310.2413111.086196.6
2.31-2.910.1912961.049193.1
2.91-900.1113211.039195.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine beta strands with ideal geometry

Resolution: 2→21.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.375 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.265 40 4.9 %RANDOM
Rwork0.201 ---
obs0.205 820 83.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.338 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20.41 Å20.99 Å2
2--0.34 Å2-0.09 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 2→21.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms200 0 0 4 204
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023200
X-RAY DIFFRACTIONr_bond_other_d00.02208
X-RAY DIFFRACTIONr_angle_refined_deg2.2712.106272
X-RAY DIFFRACTIONr_angle_other_deg3.1193472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.878520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.309258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0761532
X-RAY DIFFRACTIONr_chiral_restr0.0360.236
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02204
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0236
X-RAY DIFFRACTIONr_nbd_refined0.2240.228
X-RAY DIFFRACTIONr_nbd_other0.2530.2159
X-RAY DIFFRACTIONr_nbtor_refined0.2140.281
X-RAY DIFFRACTIONr_nbtor_other0.1360.2103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2870.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.210
X-RAY DIFFRACTIONr_mcbond_it5.5741.5120
X-RAY DIFFRACTIONr_mcbond_other01.556
X-RAY DIFFRACTIONr_mcangle_it6.9522188
X-RAY DIFFRACTIONr_scbond_it7.371380
X-RAY DIFFRACTIONr_scangle_it10.1864.584
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.267 49 -
obs--84.48 %

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