BMRB Entry 17034

Name: 1H and 15N Chemical Shift Assignments for the Syrian hamster prion protein shPrP(90-232)
Published: 2011-01-19

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17034

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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:

1H and 15N Chemical Shift Assignments for the Syrian hamster prion protein shPrP(90-232)

Deposition date:

2010-06-30

Original release date:

2011-01-19

Authors:

Bjorndahl, Trent; Zhou, Guo-Ping; Lui, Xue-Hui; Perez-Pineiro, Rolando; Semenchenko, Valentyna; Bujold, Adina; Sobsey, Constance; Wishart, David

Citation:

Citation: Bjorndahl, Trent; Zhou, Guo-Ping; Liu, Xuehui; Perez-Pineiro, Rolando; Semenchenko, Valentyna; Saleem, Fozia; Acharya, Sandipta; Bujold, Adina; Sobsey, Constance; Wishart, David. "Detailed Biophysical Characterization of the Acid-Induced PrP(c) to PrP() Conversion Process." Biochemistry 50, 1162-1173 (2011).
PubMed: 21189021

Assembly members:

Assembly members:
shPrP, polymer, 162 residues, 18710.7 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: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
shPrP: MGSSHHHHHHSSGLVPRGSG QGGGTHNQWNKPSKPKTNMK HMAGAAAAGAVVGGLGGYML GSAMSRPMMHFGNDWEDRYY RENMNRYPNQVYYRPVDQYN NQNNFVHDCVNITIKQHTVT TTTKGENFTETDIKIMERVV EQMCTTQYQKESQAYYDGRR SS

Data sets:

assigned_chemical_shifts

Data type	Count
15N chemical shifts	544
1H chemical shifts	1791

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	shPrP(90-232)	1

Entities:

Entity 1, shPrP(90-232) 162 residues - 18710.7 Da.

1

MET

GLY

SER

HIS

2

SER

GLY

LEU

VAL

PRO

ARG

GLY

SER

GLY

3

GLN

GLY

THR

HIS

ASN

GLN

TRP

ASN

4

LYS

PRO

SER

LYS

PRO

LYS

THR

ASN

MET

LYS

5

HIS

MET

ALA

GLY

ALA

GLY

ALA

6

VAL

GLY

LEU

GLY

TYR

MET

LEU

7

GLY

SER

ALA

MET

SER

ARG

PRO

MET

HIS

8

PHE

GLY

ASN

ASP

TRP

GLU

ASP

ARG

TYR

9

ARG

GLU

ASN

MET

ASN

ARG

TYR

PRO

ASN

GLN

10

VAL

TYR

ARG

PRO

VAL

ASP

GLN

TYR

ASN

11

ASN

GLN

ASN

PHE

VAL

HIS

ASP

CYS

VAL

12

ASN

ILE

THR

ILE

LYS

GLN

HIS

THR

VAL

THR

13

THR

LYS

GLY

GLU

ASN

PHE

THR

GLU

14

THR

ASP

ILE

LYS

ILE

MET

GLU

ARG

VAL

15

GLU

GLN

MET

CYS

THR

GLN

TYR

GLN

LYS

16

GLU

SER

GLN

ALA

TYR

ASP

GLY

ARG

17

SER

Samples:

sample_1: shPrP, [U-100% 15N], 0.5 – 1.0 mM; sodium acetate 20 mM; H2O 90%; D2O 10%

sample_2: shPrP, [U-100% 15N], 0.5 – 1.0 mM; sodium acetate 20 mM; H2O 90%; D2O 10%

sample_3: shPrP, [U-100% 15N], 0.5 – 1.0 mM; sodium acetate 20 mM; H2O 90%; D2O 10%

sample_4: shPrP, [U-100% 15N], 0.5 – 1.0 mM; Formic Acetate 20 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.02 M; pH: 5.2; pressure: 1 atm; temperature: 303 K

sample_conditions_2: ionic strength: 0.02 M; pH: 3.5; pressure: 1 atm; temperature: 303 K

sample_conditions_3: ionic strength: 0.02 M; pH: 3.2; pressure: 1 atm; temperature: 303 K

sample_conditions_4: ionic strength: 0.02 M; pH: 3.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
3D HNHA	sample_2	isotropic	sample_conditions_2
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_2
2D 1H-15N HSQC	sample_3	isotropic	sample_conditions_3
3D HNHA	sample_3	isotropic	sample_conditions_3
3D 1H-15N TOCSY	sample_3	isotropic	sample_conditions_3
3D 1H-15N NOESY	sample_3	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_4	isotropic	sample_conditions_4
3D HNHA	sample_4	isotropic	sample_conditions_4
3D 1H-15N TOCSY	sample_4	isotropic	sample_conditions_4
3D 1H-15N NOESY	sample_4	isotropic	sample_conditions_4

Software:

NMRView vNMRViewJ v. 8.0.a21, Johnson, One Moon Scientific - chemical shift assignment, peak picking

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

VNMRJ v2.1b, Varian - collection

NMR spectrometers:

Varian INOVA 500 MHz

BMRB	17834 4307
PDB	1B10 2LH8 4YXL
GB	AAA37090 AAA37091 AAA37092 AAA37093 AAB25731
REF	XP_005068717 XP_012967855
SP	P04273
AlphaFold	P04273