BMRB Entry 19268

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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/BMR19268
MolProbity Validation Chart

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Title:
SOLUTION NMR STRUCTURE OF THE V209M VARIANT OF THE HUMAN PRION PROTEIN (RESIDUES 90-231)
Deposition date:
2013-05-28
Original release date:
2013-09-10
Authors:
Mills, J.; Surewicz, K.; Surewicz, W.; Soennichsen, F.
Citation:

Citation: Kong, Qingzhong; Mills, Jeffrey; Kundu, Bishwajit; Li, Xinyi; Qing, Liuting; Surewicz, Krystyna; Cali, Ignazio; Huang, Shenghai; Zheng, Mengjie; Swietnicki, Wieslaw; Soennichsen, Frank; Gambetti, Pierluigi; Surewicz, Witold. "Thermodynamic Stabilization of the Folded Domain of Prion Protein Inhibits Prion Infection in Vivo"  Cell Rep. 4, 248-254 (2013).
PubMed: 23871665

Assembly members:

Assembly members:
MAJOR_PRION_PROTEIN, polymer, 146 residues, 16557.500 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: ESCHERICHIA COLI   Vector: HUPRP

Entity Sequences (FASTA):

Entity Sequences (FASTA):
MAJOR_PRION_PROTEIN: GSDPGQGGGTHSQWNKPSKP KTNMKHMAGAAAAGAVVGGL GGYMLGSAMSRPIIHFGSDY EDRYYRENMHRYPNQVYYRP MDEYSNQNNFVHDCVNITIK QHTVTTTTKGENFTETDVKM MERMVEQMCITQYERESQAY YQRGSS

Data sets:
Data typeCount
13C chemical shifts425
15N chemical shifts160
1H chemical shifts918

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1MAJOR PRION PROTEIN1

Entities:

Entity 1, MAJOR PRION PROTEIN 146 residues - 16557.500 Da.

1   GLYSERASPPROGLYGLNGLYGLYGLYTHR
2   HISSERGLNTRPASNLYSPROSERLYSPRO
3   LYSTHRASNMETLYSHISMETALAGLYALA
4   ALAALAALAGLYALAVALVALGLYGLYLEU
5   GLYGLYTYRMETLEUGLYSERALAMETSER
6   ARGPROILEILEHISPHEGLYSERASPTYR
7   GLUASPARGTYRTYRARGGLUASNMETHIS
8   ARGTYRPROASNGLNVALTYRTYRARGPRO
9   METASPGLUTYRSERASNGLNASNASNPHE
10   VALHISASPCYSVALASNILETHRILELYS
11   GLNHISTHRVALTHRTHRTHRTHRLYSGLY
12   GLUASNPHETHRGLUTHRASPVALLYSMET
13   METGLUARGMETVALGLUGLNMETCYSILE
14   THRGLNTYRGLUARGGLUSERGLNALATYR
15   TYRGLNARGGLYSERSER

Samples:

sample_1: MAJOR PRION PROTEIN, [U-99% 13C; U-99% 15N], 1.0 mM; sodium acetate 10 mM; sodium azide 0.005 w/v; H2O 95%; D2O 5%

sample_2: MAJOR PRION PROTEIN, [U-5% 13C; U-99% 15N], 1.0 mM; sodium acetate 10 mM; sodium azide 0.005 w/v; H2O 95%; D2O 5%

sample_conditions_1: ionic strength: 10 mM; pH: 4.6; pressure: 1 atm; temperature: 299 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC ALIPHATICsample_1isotropicsample_conditions_1
2D 1H-13C HSQC AROMATICsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HCCHsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1

Software:

VNMR, Varian - collection

PROSA, Guntert - processing

XEASY, Bartels et al. -

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization

Molmol, Koradi, Billeter and Wuthrich - data analysis

TOPSPIN, Bruker Biospin - collection

NMR spectrometers:

  • VARIAN INOVA 500 MHz
  • BRUKER AVANCE 600 MHz
  • Bruker Avance 800 MHz
  • Varian INOVA 900 MHz

Related Database Links:

BMRB 15676 16743 16757 17714 17756 17757 17780 18426 18550 4379 4402 4434 4620 4641 4736
PDB
DBJ BAF62360 BAG32276 BAG32278 BAG52189 BAG56832
EMBL CAA58442 CAG46836
GB AAA60182 AAA68632 AAB59442 AAB59443 AAC05365
REF NP_000302 NP_001009093 NP_001073590 NP_001073591 NP_001073592
SP P04156 P61766 P61767 P61768
AlphaFold P04156 P61766 P61767 P61768

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