BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 17166

Title: Prion-like conversion during amyloid formation at atomic resolution   PubMed: 21255727

Deposition date: 2010-09-03 Original release date: 2011-02-04

Authors: Eichner, Timo; Kalverda, Arnout; Thompson, Gary; Homans, Steve; Radford, Sheena

Citation: Eichner, Timo; Kalverda, Arnout; Thompson, Gary; Homans, Steve; Radford, Sheena. "Conformational Conversion during Amyloid Formation at Atomic Resolution"  Mol. Cell. 41, 161-172 (2011).

Assembly members:
dN6, polymer, 94 residues, 11138.4564 Da.

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
dN6: MIQVYSRHPAENGKSNFLNC YVSGFHPSDIEVDLLKNGER IEKVEHSDLSFSKDWSFYLL YYTEFTPTEKDEYACRVNHV TLSQPKIVKWDRDM

Data sets:
Data typeCount
13C chemical shifts423
15N chemical shifts97
1H chemical shifts650

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1dN61

Entities:

Entity 1, dN6 94 residues - 11138.4564 Da.

1   METILEGLNVALTYRSERARGHISPROALA
2   GLUASNGLYLYSSERASNPHELEUASNCYS
3   TYRVALSERGLYPHEHISPROSERASPILE
4   GLUVALASPLEULEULYSASNGLYGLUARG
5   ILEGLULYSVALGLUHISSERASPLEUSER
6   PHESERLYSASPTRPSERPHETYRLEULEU
7   TYRTYRTHRGLUPHETHRPROTHRGLULYS
8   ASPGLUTYRALACYSARGVALASNHISVAL
9   THRLEUSERGLNPROLYSILEVALLYSTRP
10   ASPARGASPMET

Samples:

15N13C: dN6, [U-100% 13C; U-100% 15N], 0.5 ± 5e-05 mM; sodium phosphate 25.0 ± 0.0025 mM; sodium acide 1.0 ± 0.0001 mM; H2O 90%; D2O 10%

15N13C_d2o: dN6, [U-100% 13C; U-100% 15N], 1.0 ± 0.0001 mM; sodium phosphate 25.0 ± 0.0025 mM; sodium acide 1.0 ± 0.0001 mM; D2O 100%

Structure: ionic strength: 0.040 M; pH: 7.500; pressure: 1.000 atm; temperature: 298.000 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQC/HMQC15N13CisotropicStructure
3D HNCA15N13CisotropicStructure
3D HNCACB15N13CisotropicStructure
CBCACONH (H[N[co[{CA|ca[C]}]]])15N13CisotropicStructure
3D HN(CO)CA15N13CisotropicStructure
3D HNCO15N13CisotropicStructure
3D HCCH-TOCSY15N13CisotropicStructure
3D HCCH-COSY15N13CisotropicStructure
2D 1H-13C HSQC/HMQC15N13CisotropicStructure
2D 1H-13C HSQC/HMQC15N13CisotropicStructure
C_TOCSY (hC_CH.TOCSY)15N13CisotropicStructure
3D HCCH-TOCSY15N13CisotropicStructure
3D 1H-13C NOESY15N13C_d2oisotropicStructure
2D 1H-13C HSQC/HMQC15N13CisotropicStructure
2D 1H-13C HSQC/HMQC15N13C_d2oisotropicStructure
3D 1H-13C NOESY15N13C_d2oisotropicStructure
3D 1H-15N NOESY15N13CisotropicStructure
15NNOESY_CORR15N13C_d2osolutionStructure
HNCA15N13C_d2osolutionStructure

Software:

ARIA v2.1, Linge, O'Donoghue and Nilges - refinement

AutoDep v4.3, PDBe - collection

ANALYSIS v2.1, CCPN - data analysis

NMRPipe v2.5, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRView v5.22, Johnson, One Moon Scientific - data analysis

PASD_algorithm v1.0, Kuszewski et al. - de novo structure calculation

VNMR v6.1c, VARIAN - collection

VNMR_6.1C vany, Varian - collection

X-PLOR NIH v2.17, Schwieters, Kusyewski, Tjandra and Clore - structure solution

NMR spectrometers:

  • Varian INOVA 749 MHz
  • Varian INOVA 500 MHz
  • Varian INOVA 600 MHz
  • Varian IVANOVA 749 MHz

Related Database Links:

UNP B2MG_HUMAN
BMRB 15480 16587 17165 19099 19113 19116 19118 19119 19120 19121 19122 19123 3078 3079
PDB
DBJ BAA35182 BAG38125 BAG64583 BAG72952
EMBL CAA23830 CAG33347 CAH92078
GB AAA51811 AAA87972 AAA88008 AAB25312 AAB35347
REF NP_001009066 NP_001127503 NP_004039 XP_004056148 XP_004056149
SP P16213 P61769 P61770 P61771

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts