BMRB Entry 18426

Name: Solution-state NMR structure of the human prion protein
Published: 2012-06-18

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PDB ID: 2lsb
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR18426
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution-state NMR structure of the human prion protein

Deposition date:

2012-04-26

Original release date:

2012-06-18

Authors:

Biljan, Ivana; Ilc, Gregor; Giancin, Gabriele; Zhukov, Igor; Plavec, Janez; Legname, Guiseppe

Citation:

Citation: Biljan, Ivana; Giachin, Gabriele; Ilc, Gregor; Zhukov, Igor; Plavec, Janez; Legname, Giuseppe. "Structural basis for the protective effect of the human prion protein carrying the dominant-negative E219K polymorphism." Biochem. J. 446, 243-251 (2012).
PubMed: 22676969

Assembly members:

Assembly members:
entity, polymer, 142 residues, 16169.103 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: pProExHTa

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GQGGGTHSQWNKPSKPKTNM KHMAGAAAAGAVVGGLGGYM LGSAMSRPIIHFGSDYEDRY YRENMHRYPNQVYYRPMDEY SNQNNFVHDCVNITIKQHTV TTTTKGENFTETDVKMMERV VEQMCITQYERESQAYYQRG SS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	461
15N chemical shifts	150
1H chemical shifts	930

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	human prion protein	1

Entities:

Entity 1, human prion protein 142 residues - 16169.103 Da.

1

GLY

GLN

GLY

THR

HIS

SER

GLN

TRP

2

ASN

LYS

PRO

SER

LYS

PRO

LYS

THR

ASN

MET

3

LYS

HIS

MET

ALA

GLY

ALA

GLY

4

ALA

VAL

GLY

LEU

GLY

TYR

MET

5

LEU

GLY

SER

ALA

MET

SER

ARG

PRO

ILE

6

HIS

PHE

GLY

SER

ASP

TYR

GLU

ASP

ARG

TYR

7

TYR

ARG

GLU

ASN

MET

HIS

ARG

TYR

PRO

ASN

8

GLN

VAL

TYR

ARG

PRO

MET

ASP

GLU

TYR

9

SER

ASN

GLN

ASN

PHE

VAL

HIS

ASP

CYS

10

VAL

ASN

ILE

THR

ILE

LYS

GLN

HIS

THR

VAL

11

THR

LYS

GLY

GLU

ASN

PHE

THR

12

GLU

THR

ASP

VAL

LYS

MET

GLU

ARG

VAL

13

VAL

GLU

GLN

MET

CYS

ILE

THR

GLN

TYR

GLU

14

ARG

GLU

SER

GLN

ALA

TYR

GLN

ARG

GLY

15

SER

Samples:

sample_1: huPrP, [U-100% 13C; U-100% 15N], 1.5 mM; H2O 90%; D2O 10%

sample_2: huPrP, [U-100% 13C; U-100% 15N], 1.5 mM; D2O 100%

sample_conditions_1: ionic strength: 0.1 M; pH: 5.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.1 M; pD: 5.9; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_2
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_2

Software:

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

SPARKY, Goddard - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

YASARA, (YASARA) - refinement

NMR spectrometers:

Varian Uniform NMR System 800 MHz

BMRB	15676 16743 16757 17714 17756 17757 17780 18550 19268 4379 4402 4434 4620 4641 4736
PDB	1E1G 1E1J 1E1P 1E1S 1E1U 1E1W 1FKC 1FO7 1H0L 1HJM 1HJN 1I4M 1QLX 1QLZ 1QM0 1QM1 1QM2 1QM3 2K1D 2KUN 2LEJ 2LFT 2LSB 2LV1 2M8T 2W9E 3HAF 3HAK 3HEQ 3HER 3HES 3HJ5 3HJX 4DGI 4KML 4N9O
DBJ	BAA00011 BAF62360 BAG32276 BAG32277 BAG32278
EMBL	CAA58442 CAG46836 CAG46869 CAH92912
GB	AAA19664 AAA60182 AAA68632 AAA68633 AAB59442
REF	NP_000302 NP_001009093 NP_001073590 NP_001073591 NP_001073592
SP	P04156 P40252 P40256 P61766 P61767
TPE	CAJ43808
AlphaFold	P04156 P40252 P40256 P61766 P61767