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BMRB: 17558

2LBG

Structure of the CHR of the Prion protein in DPC Micelles

Authors

Sauve, S., Aubin, Y.

Assembly

CHR/DPC micelle

Entity

1. PrP Conserved Hydrophobic Domain (polymer, Thiol state: not present), 27 monomers, 2491.911 Da Detail

KHMAGAAAAG AVVGGLGGYM LGSAMSR

2. DPV (non-polymer, Thiol state: not present), 351.462 Da

Total weight

2843.3728 Da

Max. entity weight

2491.911 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 85.9 %, Completeness (bb): 94.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.9 % (220 of 256)	82.0 % (105 of 128)	89.1 % (90 of 101)	92.6 % (25 of 27)
Backbone	94.4 % (153 of 162)	95.1 % (58 of 61)	94.6 % (70 of 74)	92.6 % (25 of 27)
Sidechain	75.4 % (86 of 114)	70.1 % (47 of 67)	83.0 % (39 of 47)
Aromatic	66.7 % (8 of 12)	66.7 % (4 of 6)	66.7 % (4 of 6)
Methyl	100.0 % (30 of 30)	100.0 % (15 of 15)	100.0 % (15 of 15)

1. PrP Conserved Hydrophobic Domain

KHMAGAAAAG AVVGGLGGYM LGSAMSR

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LBG, Strand ID: A Detail

Release date

2011-12-04

Citation

Interactions between the conserved hydrophobic region of the prion protein and dodecylphosphocholine micelles
Sauve, S., Buijs, D., Gingras, G., Aubin, Y.
J. Biol. Chem. (2012), 287, 1915-1922, PubMed 22128151 , DOI 10.1074/jbc.M111.279364 , Abstract

Related entities 1. PrP Conserved Hydrophobic Domain, : 1 : 43 : 38 : 1 : 1 entities Detail

Interaction partners 1. PrP Conserved Hydrophobic Domain, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

3 3D HNCO

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

4 3D HNCA

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

5 3D HNCACB

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

6 3D HBHA(CO)NH

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

7 3D HNHA

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

8 3D HCCH-TOCSY

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

9 3D HCCH-COSY

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

11 3D 1H-13C NOESY

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

12 3D CBCA(CO)NH

Instrument

Bruker Avance III - 600 MHz triple resonance cryogenic probehead

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 310 K, pH 7.6, Details 1.5 mg of 13C 15N PrP110-136 in 14mg of DPC

#	Name	Isotope labeling	Type	Concentration
1	PrP Conserved Hydrophobic Domain	[U-99% 13C; U-99% 15N]		1.5 mg
2	Dodecylphosphocholine (DPC) Micelle	natural abundance		14 mg
3	sodium phosphate	natural abundance		10 mM
4	DSS	natural abundance		1 mM
5	H2O	natural abundance		95 %
6	D2O	natural abundance		5 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_17558_2lbg.nef
Input source #2: Coordindates	2lbg.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

None

Sequence alignments

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

--------10--------20-------
KHMAGAAAAGAVVGGLGGYMLGSAMSR
|||||||||||||||||||||||||||
KHMAGAAAAGAVVGGLGGYMLGSAMSR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	27	0	0	100.0

Content subtype: combined_17558_2lbg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	220		100.0 (chain: A, length: 27)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	244 (1)	noe	96.3 (chain: A, length: 27)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 105
  - ¹³C chemical shifts: 90
  - ¹⁵N chemical shifts: 25
- Completeness of assignments
  - Entity_assemble_ID: A
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 27, Sequence coverage: 96.3%
- Total number of restraints: 244
- Weight of restraints: 1.0 (244)
- Potential type of restraints: upper-bound-parabolic (244)
- Range of distance target values: 1.79, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords Conserved Hydrophobic Domain, Prion protein, PrP, Conserved Hydrophobic region of the Prion protein