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- PDB-8yg2: Crystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Is... -

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Basic information

Entry
Database: PDB / ID: 8yg2
TitleCrystal structure of amyloidogenic peptide Piv-NFGAIL-NH2 from Islet Amyloid Polypeptide
ComponentsAmyloidogenic peptide from Islet Amyloid Polypeptide
KeywordsPROTEIN FIBRIL / Amyloid / CASL
Function / homologyFORMIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSawazaki, T. / Sasaki, D. / Sohma, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Catalysis driven by an amyloid-substrate complex.
Authors: Sawazaki, T. / Sasaki, D. / Sohma, Y.
History
DepositionFeb 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloidogenic peptide from Islet Amyloid Polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7622
Polymers7161
Non-polymers461
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint0 kcal/mol
Surface area1180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)4.864, 20.466, 20.855
Angle α, β, γ (deg.)90.00, 88.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Amyloidogenic peptide from Islet Amyloid Polypeptide


Mass: 715.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
Has ligand of interestN
Has protein modificationY

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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: 1.54 Å3/Da / Density % sol: 15.15 % / Description: Needle
Crystal growTemperature: 298 K / Method: evaporation / Details: Formic acid / PH range: 2.0-3.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.04 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.25→20.47 Å / Num. obs: 1063 / % possible obs: 91.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 59.11
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 2 % / Rmerge(I) obs: 0.155 / Num. unique obs: 55 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALS2.2.10data reduction
DIALS2.2.10data scaling
PHASER2.8.3phasing
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→20.47 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.881 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.069
RfactorNum. reflection% reflection
Rfree0.201 63 5.977 %
Rwork0.174 --
obs-1054 91.1 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 5.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.115 Å20 Å20.189 Å2
2---0.011 Å20 Å2
3---0.135 Å2
Refinement stepCycle: LAST / Resolution: 1.25→20.47 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms51 0 3 0 54
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01467
X-RAY DIFFRACTIONr_bond_other_d0.0030.01875
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9282
X-RAY DIFFRACTIONr_angle_other_deg1.0452.001157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.77756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.44626.6673
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.912155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0430.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0281
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0230
X-RAY DIFFRACTIONr_nbd_refined0.0140.23
X-RAY DIFFRACTIONr_nbd_other0.2030.237
X-RAY DIFFRACTIONr_nbtor_refined0.1870.222
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.030.21
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.230.54323
X-RAY DIFFRACTIONr_mcbond_other0.2310.6524
X-RAY DIFFRACTIONr_mcangle_it0.3760.81726
X-RAY DIFFRACTIONr_mcangle_other0.380.82527
X-RAY DIFFRACTIONr_scbond_it0.2060.67444
X-RAY DIFFRACTIONr_scbond_other0.2050.56343
X-RAY DIFFRACTIONr_scangle_it0.220.88552
X-RAY DIFFRACTIONr_scangle_other0.2190.95653
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 1 -
Rwork0.243 74 -
obs--94.94 %

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