BMRB Entry 19062

Name: Atomic-resolution structure of a cross-beta protofilament
Published: 2013-09-04

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PDB ID: 2m5n
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19062
MolProbity Validation Chart

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Atomic-resolution structure of a cross-beta protofilament PubMed: 23513222

Deposition date: 2013-02-27 Original release date: 2013-09-04

Authors: Fitzpatrick, Anthony; Debelouchina, Galia; Bayro, Marvin; Clare, Daniel; Caporini, Marc; Bajaj, Vikram; Jaroniec, Christopher; Wang, Luchun; Ladizhansky, Vladimir; Muller, Shirley; MacPhee, Cait; Waudby, Christopher; Mott, Helen; de Simone, Alfonso; Knowles, Tuomas; Saibil, Helen; Vendruscolo, Michele; Orlova, Elena; Griffin, Robert; Dobson, Christopher

Citation: Fitzpatrick, Anthony; Debelouchina, Galia; Bayro, Marvin; Clare, Daniel; Caporini, Marc; Bajaj, Vikram; Jaroniec, Christopher; Wang, Luchun; Ladizhansky, Vladimir; Muller, Shirley; MacPhee, Cait; Waudby, Christopher; Mott, Helen; De Simone, Alfonso; Knowles, Tuomas; Saibil, Helen; Vendruscolo, Michele; Orlova, Elena; Griffin, Robert; Dobson, Christopher. "Atomic structure and hierarchical assembly of a cross- amyloid fibril." Proc. Natl. Acad. Sci. U.S.A. 110, 5468-5473 (2013).

Assembly members:
protofilament_part1, polymer, 11 residues, 1198.378 Da.

Natural source: Common Name: Norway rat Taxonomy ID: 10116 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Rattus norvegicus

Experimental source: Production method: chemical synthesis Host organism: Escherichia coli

Entity Sequences (FASTA):
protofilament_part1: YTIAALLSPYS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	57
15N chemical shifts	11

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	cross-beta protofilament 1	1
2	cross-beta protofilament 2	1
3	cross-beta protofilament 3	1
4	cross-beta protofilament 4	1

Entities:

Entity 1, cross-beta protofilament 1 11 residues - 1198.378 Da.

1

TYR

THR

ILE

ALA

LEU

SER

PRO

TYR

2

SER

Samples:

sample_1: TTR(105-115), [U-100% 13C; U-100% 15N], 15 mg/mL; acetonitrile 10%; H2O 90%

sample_conditions_1: pH: 2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
1D DQ-DRAWS	sample_1	isotropic	sample_conditions_1
REDOR	sample_1	isotropic	sample_conditions_1
ZF-TEDOR	sample_1	isotropic	sample_conditions_1
2D PDSD	sample_1	isotropic	sample_conditions_1

Software:

CNSSOLVE, Brunger, Adams, Clore, Gros, Nilges and Read - structure solution

NMR spectrometers:

Bruker N/A 900 MHz
N/A N/A 750 MHz
N/A N/A 500 MHz