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BMRB: 17834

2LH8

Syrian hamster prion protein with thiamine

Authors

Perez-Pineiro, R., Bjorndahl, T.C., Berjanskii, M., Hau, D., Li, L., Huang, A., Lee, R., Gibbs, E., Ladner, C., Wei Dong, Y., Abera, A., Cashman, N.R., Wishart, D.

Assembly

shPrP, Thiamine

Entity

1. shPrP (polymer, Thiol state: free and disulfide bound), 104 monomers, 12444.68 Da Detail

LGGYMLGSAM SRPMMHFGND WEDRYYRENM NRYPNQVYYR PVDQYNNQNN FVHDCVNITI KQHTVTTTTK GENFTETDIK IMERVVEQMC TTQYQKESQA YYDG

2. VB1 (non-polymer), 349.403 Da

Total weight

12794.083 Da

Max. entity weight

12444.68 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS55:SG	1:CYS90:SG

Source organism

Mesocricetus auratus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 37.1 %, Completeness (bb): 91.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹⁵N
All	37.1 % (286 of 770)	28.5 % (185 of 650)	84.2 % (101 of 120)
Backbone	91.0 % (284 of 312)	86.7 % (183 of 211)	100.0 % (101 of 101)
Sidechain	0.4 % (2 of 458)	0.5 % (2 of 439)	0.0 % (0 of 19)
Aromatic	0.0 % (0 of 68)	0.0 % (0 of 67)	0.0 % (0 of 1)
Methyl	2.6 % (1 of 38)	2.6 % (1 of 38)

1. shPrP

LGGYMLGSAM SRPMMHFGND WEDRYYRENM NRYPNQVYYR PVDQYNNQNN FVHDCVNITI KQHTVTTTTK GENFTETDIK IMERVVEQMC TTQYQKESQA YYDG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2, Details 300 M, 350 L, 20 mM KH2PO4, pH 6.2

#	Name	Isotope labeling	Concentration
1	shPrP	[U-100% 15N]	0.3 mM
2	thiamine	natural abundance	10 mM
3	KH2PO4	natural abundance	20 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
6	shPrP	natural abundance	0.5 mM
7	thiamine	natural abundance	12.5 mM
8	H2O	natural abundance	90 %
9	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.2

#	Name	Isotope labeling	Concentration
10	shPrP	natural abundance	0.5 mM
11	thiamine	natural abundance	10 mM
12	H2O	natural abundance	90 %
13	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 1 models in PDB: 2LH8, Strand ID: A Detail

Release date

2011-09-12

Citation

The prion protein binds thiamine
Perez-Pineiro, R., Bjorndahl, T.C., Berjanskii, M.V., Hau, D., Li, L., Huang, A., Lee, R., Gibbs, E., Ladner, C., Dong, Y., Abera, A., Cashman, N.R., Wishart, D.S.
FEBS J. (2011), 278, 4002-4014, PubMed 21848803 , DOI 10.1111/j.1742-4658.2011.08304.x , Abstract

Related entities 1. shPrP, : 1 : 4 : 151 entities Detail

Interaction partners 1. shPrP, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 5 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17834_2lh8.nef
Input source #2: Coordindates	2lh8.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	VIB	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM	Distance restraints

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

----40--------50--------60--------70--------80--------90-------100-------110-------120-------130----
LGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LGGYMLGSAMSRPMMHFGNDWEDRYYRENMNRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDIKIMERVVEQMCTTQYQKESQA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----
YYDG
||||
YYDG
----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	0	0	100.0

Content subtype: combined_17834_2lh8.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	284		97.1 (chain: A, length: 104)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	7 (1)	noe	4.8 (chain: A, length: 104), 100.0 (chain: B, length: 1)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 97.1%
- Total number of assignments
  - ¹H chemical shifts: 183
  - ¹⁵N chemical shifts: 101
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	650	182	28.0
¹⁵N chemical shifts	126	101	80.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	211	182	86.3
¹⁵N chemical shifts	101	101	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	439	0	0.0
¹⁵N chemical shifts	25	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 4.8%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of restraints: 7
- Weight of restraints: 1.0 (7)
- Potential type of restraints: square-well-parabolic (7)
- Range of distance target values: 2.25, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Keywords hamster, prion, syrian, thiamine

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Found 1 Document (0.606 seconds)

BMRB: 17834

Sample #1

Sample #2

Sample #3

Related entities 1. shPrP, : 1 : 4 : 151 entities Detail

Interaction partners 1. shPrP, : 2 interactors Detail

Experiments performed 5 experiments Detail

Instrument

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NMR combined restraints 3 contents Detail