BMRB Entry 16505

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16505
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Title:
NMR structure of the octarepeat region of prion protein bound to pentosan polysulfate
Deposition date:
2009-09-21
Original release date:
2009-11-20
Authors:
Taubner, Lara; Caughey, Byron; Copie, Valerie
Citation:

Citation: Taubner, Lara; Bienkiewicz, Ewa; Copie, Valerie; Caughey, Byron. "Structure of the flexible amino-terminal domain of prion protein bound to a sulfated glycan."  J. Mol. Biol. 395, 475-490 (2010).
PubMed: 19913031

Assembly members:

Assembly members:
octarepeats, polymer, 85 residues, 3500.671 Da.

Natural source:

Natural source:   Common Name: golden hamster   Taxonomy ID: 10036   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Mesocricetus auratus

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET-41

Entity Sequences (FASTA):

Entity Sequences (FASTA):
octarepeats: MKKRPKPGGWNTGGSRYPGQ GSPGGNRYPPQGGGTWGQPH GGGWGQPHGGGWGQPHGGGW GQPHGGGWGQGGGTHNQWNK PSKPK

Data sets:
Data typeCount
13C chemical shifts160
15N chemical shifts50
1H chemical shifts261

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1octarepeats1

Entities:

Entity 1, octarepeats 85 residues - 3500.671 Da.

1   METLYSLYSARGPROLYSPROGLYGLYTRP
2   ASNTHRGLYGLYSERARGTYRPROGLYGLN
3   GLYSERPROGLYGLYASNARGTYRPROPRO
4   GLNGLYGLYGLYTHRTRPGLYGLNPROHIS
5   GLYGLYGLYTRPGLYGLNPROHISGLYGLY
6   GLYTRPGLYGLNPROHISGLYGLYGLYTRP
7   GLYGLNPROHISGLYGLYGLYTRPGLYGLN
8   GLYGLYGLYTHRHISASNGLNTRPASNLYS
9   PROSERLYSPROLYS

Samples:

sample_1: octarepeats, [U-15N], 0.5 mM; D2O, [U-2H], 5%; DMSO, [U-2H], 20%; pentosan polysulfate 20 mM; sodium acetate 10 mM; H2O 75%

sample_2: octarepeats, [U-13C; U-15N], 0.5 mM; D2O, [U-2H], 5%; DMSO, [U-2H], 20%; pentosan polysulfate 20 mM; sodium acetate 10 mM; H2O 75%

sample_3: octarepeats, [U-13C; U-15N], 0.5 mM; D2O, [U-2H], 80%; DMSO, [U-2H], 20%; pentosan polysulfate 20 mM; sodium acetate 10 mM

sample_conditions_1: pH: 5.0; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_3isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D C(CO)NHsample_2isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_3isotropicsample_conditions_1

Software:

ProcheckNMR, Laskowski and MacArthur - geometry optimization

NMRView, Johnson, One Moon Scientific - data analysis, peak picking

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

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Bruker DRX 600 MHz

Related Database Links:

BMRB 4402
PDB
DBJ BAA00011 BAA08790 BAD51981 BAE91721 BAF62360
EMBL CAG46869 CAH92912
GB AAA19664 AAA37013 AAA37014 AAA37090 AAA37091
PIR B34759
REF NP_000302 NP_001009093 NP_001040617 NP_001073590 NP_001073591
SP P04156 P04273 P13852 P40247 P40248
TPE CAJ43808
AlphaFold P04156 P04273 P13852 P40247 P40248

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks