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Basic information

Entry
Database: PDB / ID: 2kib
TitleProtein Fibril
ComponentsNFGAIL segment from human islet amyloid polypeptide
KeywordsPROTEIN FIBRIL / IAPP / Amylin / SNNFGAILSS / Symmetry
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsNielsen, J.T. / Bjerring, M. / Jeppesen, M.D. / Pedersen, R.O. / Pedersen, J.M. / Hein, K.L. / Vosegaard, T. / Skrydstrup, T. / Otzen, D.E. / Nielsen, N.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: Unique identification of supramolecular structures in amyloid fibrils by solid-state NMR spectroscopy.
Authors: Nielsen, J.T. / Bjerring, M. / Jeppesen, M.D. / Pedersen, R.O. / Pedersen, J.M. / Hein, K.L. / Vosegaard, T. / Skrydstrup, T. / Otzen, D.E. / Nielsen, N.C.
History
DepositionMay 1, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NFGAIL segment from human islet amyloid polypeptide
B: NFGAIL segment from human islet amyloid polypeptide
C: NFGAIL segment from human islet amyloid polypeptide
D: NFGAIL segment from human islet amyloid polypeptide
E: NFGAIL segment from human islet amyloid polypeptide
F: NFGAIL segment from human islet amyloid polypeptide
G: NFGAIL segment from human islet amyloid polypeptide
H: NFGAIL segment from human islet amyloid polypeptide


Theoretical massNumber of molelcules
Total (without water)5,7678
Polymers5,7678
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
NFGAIL segment from human islet amyloid polypeptide


Mass: 720.815 Da / Num. of mol.: 8 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NCA
121NCO
1312D 13C-13C DARR 2.5 ms mixing
1412D 13C-13C DARR 5 ms mixing
1512D 13C-13C DARR 20 ms mixing
1612D 13C-13C DARR 40 ms mixing
1712D 13C-13C DARR 100 ms mixing
1812D 13C-13C DARR 200 ms mixing

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Sample preparation

DetailsContents: 2.5 mg/mL [U-100% 13C; U-100% 15N] NFGAIL, 100% H2O
Solvent system: 100% H2O
SampleConc.: 2.5 mg/mL / Component: NFGAIL / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionspH: 7.2 / Pressure: ambient / Temperature: 263 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz

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Processing

NMR softwareName: X-PLOR NIH / Version: 2.18 / Developer: Schwieters, C.D. et al. / Classification: refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 10
NMR ensemble rmsDistance rms dev: 0.049 Å

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