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- PDB-5ugk: Zinc-Binding Structure of a Catalytic Amyloid from Solid-State NM... -

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Basic information

Entry
Database: PDB / ID: 5ugk
TitleZinc-Binding Structure of a Catalytic Amyloid from Solid-State NMR Spectroscopy
ComponentsILE-HIS-VAL-HIS-LEU-GLN-ILE
KeywordsMETAL BINDING PROTEIN / Amyloid
Biological speciessynthetic construct (others)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsLee, M. / Wang, T. / Makhlynets, O.V. / Wu, Y. / Polizzi, N. / Wu, H. / Gosavi, P.M. / Korendovych, I.V. / DeGrado, W.F. / Hong, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM066976 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119634 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)P01AG002132 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Zinc-binding structure of a catalytic amyloid from solid-state NMR.
Authors: Lee, M. / Wang, T. / Makhlynets, O.V. / Wu, Y. / Polizzi, N.F. / Wu, H. / Gosavi, P.M. / Stohr, J. / Korendovych, I.V. / DeGrado, W.F. / Hong, M.
History
DepositionJan 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 28, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / pdbx_nmr_software
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name
Revision 1.5Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.6May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ILE-HIS-VAL-HIS-LEU-GLN-ILE
C: ILE-HIS-VAL-HIS-LEU-GLN-ILE
E: ILE-HIS-VAL-HIS-LEU-GLN-ILE
G: ILE-HIS-VAL-HIS-LEU-GLN-ILE
I: ILE-HIS-VAL-HIS-LEU-GLN-ILE
K: ILE-HIS-VAL-HIS-LEU-GLN-ILE
O: ILE-HIS-VAL-HIS-LEU-GLN-ILE
Q: ILE-HIS-VAL-HIS-LEU-GLN-ILE
S: ILE-HIS-VAL-HIS-LEU-GLN-ILE
U: ILE-HIS-VAL-HIS-LEU-GLN-ILE
W: ILE-HIS-VAL-HIS-LEU-GLN-ILE
Y: ILE-HIS-VAL-HIS-LEU-GLN-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,11724
Polymers10,33312
Non-polymers78512
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide
ILE-HIS-VAL-HIS-LEU-GLN-ILE


Mass: 861.042 Da / Num. of mol.: 12 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 13C-13C correlation spectra
121isotropic12D 15N-13C correlation spectra
131isotropic1REDOR
142isotropic12D 13C-13C correlation spectra

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid10.4 g/L [U-13C; U-15N] IVL, pH 8 Tris buffer13C, 15N-labeled IVL fibril sample with Zn2+IVL-labeled HHQpH 8 Tris buffer
solid20.4 g/L [U-13C] mixed sample, pH 8 Tris bufferMixed labeled fibrils (samples 3, 4, 9 and 10) for determining intermolecular packing were prepared using a urea-based solubilization protocol to ensure complete mixing.Mixed labeled fibrilspH 8 Tris buffer
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 g/LIVL[U-13C; U-15N]1
0.4 g/Lmixed sample[U-13C]2
Sample conditionsIonic strength: 100 mM / Label: 1 / pH: 8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Bruker / Manufacturer: Bruker / Model: Bruker / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospinchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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