BMRB Entry 17834

Name: Syrian hamster prion protein with thiamine
Published: 2011-09-13

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PDB ID: 2lh8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR17834
MolProbity Validation Chart

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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:

Syrian hamster prion protein with thiamine

Deposition date:

2011-08-05

Original release date:

2011-09-13

Authors:

Perez-Pineiro, Rolando; Bjorndahl, Trent; Berjanskii, Mark; Hau, David; Li, Li; Huang, Alan; Lee, Rose; Gibbs, Ebrima; Ladner, Carol; Wei Dong, Ying; Abera, Ashenafi; Cashman, Neil; Wishart, David

Citation:

Citation: Perez-Pineiro, Rolando; Bjorndahl, Trent; Berjanskii, Mark; Hau, David; Li, Li; Huang, Alan; Lee, Rose; Gibbs, Ebrima; Ladner, Carol; Dong, Ying Wei; Abera, Ashenafi; Cashman, Neil; Wishart, David. "The Prion Protein Binds Thiamine" FEBS J. 278, 4002-4014 (2011).
PubMed: 21848803

Assembly members:

Assembly members:
shPrP, polymer, 104 residues, 12457.871 Da.
VB1, non-polymer, 349.403 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: LGGYMLGSAMSRPMMHFGND WEDRYYRENMNRYPNQVYYR PVDQYNNQNNFVHDCVNITI KQHTVTTTTKGENFTETDIK IMERVVEQMCTTQYQKESQA YYDG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
15N chemical shifts	101
1H chemical shifts	183

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	shPrP	1
2	Thiamine	2

Entities:

Entity 1, shPrP 104 residues - 12457.871 Da.

1

LEU

GLY

TYR

MET

LEU

GLY

SER

ALA

MET

2

SER

ARG

PRO

MET

HIS

PHE

GLY

ASN

ASP

3

TRP

GLU

ASP

ARG

TYR

ARG

GLU

ASN

MET

4

ASN

ARG

TYR

PRO

ASN

GLN

VAL

TYR

ARG

5

PRO

VAL

ASP

GLN

TYR

ASN

GLN

ASN

6

PHE

VAL

HIS

ASP

CYS

VAL

ASN

ILE

THR

ILE

7

LYS

GLN

HIS

THR

VAL

THR

LYS

8

GLY

GLU

ASN

PHE

THR

GLU

THR

ASP

ILE

LYS

9

ILE

MET

GLU

ARG

VAL

GLU

GLN

MET

CYS

10

THR

GLN

TYR

GLN

LYS

GLU

SER

GLN

ALA

11

TYR

ASP

GLY

Entity 2, Thiamine - C13 H23 N3 O6 S - 349.403 Da.

1

VB1

Samples:

sample_1: shPrP, [U-100% 15N], 0.3 mM; thiamine 10 mM; KH2PO4 20 mM; H2O 90%; D2O 10%

sample_2: shPrP 0.5 mM; thiamine 12.5 mM; H2O 90%; D2O 10%

sample_3: shPrP 0.5 mM; thiamine 10 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.02 M; pH: 6.2; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
1D STD-TOCSY	sample_2	isotropic	sample_conditions_1
2D NOESY	sample_3	isotropic	sample_conditions_1

Software:

NMRDraw v3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

VNMRJ, Varian - collection

NMRView, Johnson, One Moon Scientific - chemical shift assignment, data analysis, peak picking

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

NMR spectrometers:

Varian INOVA 500 MHz
Varian INOVA 800 MHz

BMRB	17034 4307
PDB	1B10 2LH8 4YXL
GB	AAA37090 AAA37091 AAA37092 AAA37093 AAB25731
REF	XP_005068717 XP_012967855
SP	P04273
AlphaFold	P04273