BMRB Entry 16743

Name: Three dimensional structure of HuPrP(90-231 M129 Q212P)
Published: 2010-09-02

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PDB ID: 2kun
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16743
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Three dimensional structure of HuPrP(90-231 M129 Q212P)

Deposition date:

2010-02-23

Original release date:

2010-09-02

Authors:

Ilc, Gregor; Giachin, Gabriele; Jaremko, Mariusz; Jaremko, Lukasz; Zhukov, Igor; Plavec, Janez; Legname, Guiseppe

Citation:

Citation: Ilc, Gregor; Giachin, Gabriele; Jaremko, Mariusz; Jaremko, Lukasz; Benetti, Federico; Plavec, Janez; Zhukov, Igor; Legname, Guiseppe. "NMR structure of the human prion protein with the pathological Q212P mutation reveals unique structural features" PLoS One 5, e11715-e11715 (2010).
PubMed: 20661422

Assembly members:

Assembly members:
HuPrP(90-231 M129 Q212P), polymer, 148 residues, 16966.982 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: pET-11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
HuPrP(90-231 M129 Q212P): GQGGGTHSQWNKPSKPKTNM KHMAGAAAAGAVVGGLGGYM LGSAMSRPIIHFGSDYEDRY YRENMHRYPNQVYYRPMDEY SNQNNFVHDCVNITIKQHTV TTTTKGENFTETDVKMMERV VEPMCITQYERESQAYYQRG SSHHHHHH

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	610
15N chemical shifts	147
1H chemical shifts	942

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	HuPrP(90-231 M129 Q212P)	1

Entities:

Entity 1, HuPrP(90-231 M129 Q212P) 148 residues - 16966.982 Da.

His-Tag6 on C-terminus

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

PRO

MET

CYS

ILE

THR

GLN

TYR

GLU

14

ARG

GLU

SER

GLN

ALA

TYR

GLN

ARG

GLY

15

SER

HIS

Samples:

sample_1: PrP(Q212P), [U-98% 13C; U-98% 15N], 1.0 mM; H2O 90%; D2O 10%; NaCl 150 mM

sample_2: PrP(Q212P), [U-98% 13C; U-98% 15N], 1.0 mM; D2O 100%; NaCl 150 mM

sample_conditions_1: ionic strength: 150 mM; pH: 5.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 150 mM; pH: 5.1; pressure: 1 atm; 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 HN(CO)CA	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 1H-13C NOESY	sample_2	isotropic	sample_conditions_2
3D CCH-TOCSY	sample_2	isotropic	sample_conditions_2

Software:

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

SPARKY, Goddard - chemical shift assignment, data analysis, peak picking

CYANA, Guntert, Mumenthaler and Wuthrich - structure solution

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

CARA, Keller and Wuthrich - chemical shift assignment

NMR spectrometers:

Varian Uniform NMR System 800 MHz
Varian Uniform NMR System 700 MHz

BMRB	15676 16757 17714 17756 17757 17780 18426 18550 19268 4379 4402 4434 4620 4641 4736
PDB	1E1G 1E1J 1E1P 1E1S 1E1U 1E1W 1FKC 1FO7 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
GB	AAA19664 AAA60182 AAA68632 AAA68633 AAB59442
REF	NP_000302 NP_001009093 NP_001073590 NP_001073591 NP_001073592
SP	P04156 P40252 P61766 P61767 P61768
AlphaFold	P04156 P40252 P61766 P61767 P61768