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BMRB: 15676

2K1D

NMR Studies of a Pathogenic Mutant (D178N) of the Human Prion Protein

Authors

Mills, J.L., Surewicz, K., Surewicz, W.K., Sonnichsen, F.D.

Assembly

prion protein

Entity

1. prion protein (polymer, Thiol state: all disulfide bound), 146 monomers, 16471.09 Da Detail

GSDPGQGGGT HSQWNKPSKP KTNMKHMAGA AAAGAVVGGL GGYVLGSAMS RPIIHFGSDY EDRYYRENMH RYPNQVYYRP MDEYSNQNNF VHNCVNITIK QHTVTTTTKG ENFTETDVKM MERVVEQMCI TQYERESQAY YQRGSS

Formula weight

16471.09 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS94:SG	1:CYS129:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, TORSION ANGLE DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 75.3 %, Completeness: 61.3 %, Completeness (bb): 59.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	61.3 % (1019 of 1661)	65.3 % (566 of 867)	53.3 % (338 of 634)	71.9 % (115 of 160)
Backbone	59.4 % (513 of 864)	65.8 % (198 of 301)	50.8 % (215 of 423)	71.4 % (100 of 140)
Sidechain	64.4 % (598 of 928)	65.0 % (368 of 566)	62.9 % (215 of 342)	75.0 % (15 of 20)
Aromatic	48.1 % (74 of 154)	61.0 % (47 of 77)	35.5 % (27 of 76)	0.0 % (0 of 1)
Methyl	76.4 % (81 of 106)	75.5 % (40 of 53)	77.4 % (41 of 53)

1. V129/D178N prion protein

GSDPGQGGGT HSQWNKPSKP KTNMKHMAGA AAAGAVVGGL GGYVLGSAMS RPIIHFGSDY EDRYYRENMH RYPNQVYYRP MDEYSNQNNF VHNCVNITIK QHTVTTTTKG ENFTETDVKM MERVVEQMCI TQYERESQAY YQRGSS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6

#	Name	Isotope labeling	Concentration
1	V129/D178N prion protein	[U-99% 13C; U-99% 15N]	350 uM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	100 uM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.06 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K1D, Strand ID: A Detail

Release date

2009-11-29

Citation

Community- and ecosystem-level effects of multiple environmental change drivers: beyond null model testing
Mills, J.L., Surewicz, K., Surewicz, W.K., Sonnichsen, F.D.
Glob. Chang. Biol. (2018), PubMed 29959825 , DOI 10.1111/gcb.14382 , Abstract

Related entities 1. prion protein, : 1 : 1 : 99 entities Detail

Interaction partners 1. prion protein, : 73 interactors Detail

More details for 73 interactors identified by 15 citations

Experiments performed 8 experiments Detail

1 2D 1H-15N HSQC