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BMRB: 25251

2MV9

Solution structure of Ovis Aries PrP with mutation delta193-196

Authors

Munoz, C., Egalon, A., Beringue, V., Rezaei, H., Dron, M., Sizun, C.

Assembly

PrPdelta193-196

Entity

1. PrPdelta193-196 (polymer, Thiol state: all disulfide bound), 150 monomers, 17109.95 Da Detail

MGSSHHHHHH SSGLVPRGSH MSNKPSKPKT NMKHVAGAAA AGAVVGGLGG YMLGSVMSRP LIHFGNDYED RYYRENMYRY PNQVYYRPVD QYSNQNNFVH DCVNITVKQH TVKGENFTET DIKIMERVVE QMCITQYQRE SQAYYQRGAS

Formula weight

17109.95 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS102:SG	1:CYS133:SG

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.0 %, Completeness: 60.6 %, Completeness (bb): 67.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	60.6 % (1048 of 1730)	76.5 % (691 of 903)	31.5 % (209 of 664)	90.8 % (148 of 163)
Backbone	67.1 % (596 of 888)	89.9 % (276 of 307)	43.0 % (188 of 437)	91.7 % (132 of 144)
Sidechain	49.1 % (481 of 979)	69.6 % (415 of 596)	13.7 % (50 of 364)	84.2 % (16 of 19)
Aromatic	36.5 % (62 of 170)	67.1 % (57 of 85)	5.9 % (5 of 85)
Methyl	55.2 % (64 of 116)	94.8 % (55 of 58)	15.5 % (9 of 58)

1. PrPdelta193-196

MGSSHHHHHH SSGLVPRGSH MSNKPSKPKT NMKHVAGAAA AGAVVGGLGG YMLGSVMSRP LIHFGNDYED RYYRENMYRY PNQVYYRPVD QYSNQNNFVH DCVNITVKQH TVKGENFTET DIKIMERVVE QMCITQYQRE SQAYYQRGAS

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.15 (±2.0E-5) mM
2	Sodium acetate	natural abundance		10.00 (±0.001) mM
3	H2O	natural abundance		90 (±0.001) mM
4	D2O	natural abundance		10 (±0.001) mM

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-99% 15N]		0.46 (±2.0E-5) mM
6	Sodium acetate	natural abundance		10.00 (±0.001) mM
7	H2O	natural abundance		90 (±0.001) mM
8	D2O	natural abundance		10 (±0.001) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 2MV9, Strand ID: A Detail

Release date

2015-10-04

Citation

Conversion ability of prion protein helix 2 deletion mutants
Munoz, C., Sizun, C., Egalon, A., Beringue, V., Rezaei, H., Dron, M.
Not known

Related entities 1. PrPdelta193-196, : 1 : 106 entities Detail

Interaction partners 1. PrPdelta193-196, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 8 experiments Detail

1 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.15 (±2.0E-5) mM
2	Sodium acetate	natural abundance		10.00 (±0.001) mM
3	H2O	natural abundance		90 (±0.001) mM
4	D2O	natural abundance		10 (±0.001) mM

2 3D HN(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.15 (±2.0E-5) mM
2	Sodium acetate	natural abundance		10.00 (±0.001) mM
3	H2O	natural abundance		90 (±0.001) mM
4	D2O	natural abundance		10 (±0.001) mM

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.15 (±2.0E-5) mM
2	Sodium acetate	natural abundance		10.00 (±0.001) mM
3	H2O	natural abundance		90 (±0.001) mM
4	D2O	natural abundance		10 (±0.001) mM

4 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-99% 15N]		0.46 (±2.0E-5) mM
6	Sodium acetate	natural abundance		10.00 (±0.001) mM
7	H2O	natural abundance		90 (±0.001) mM
8	D2O	natural abundance		10 (±0.001) mM

5 3D 1H-15N TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-99% 15N]		0.46 (±2.0E-5) mM
6	Sodium acetate	natural abundance		10.00 (±0.001) mM
7	H2O	natural abundance		90 (±0.001) mM
8	D2O	natural abundance		10 (±0.001) mM

6 2D 1H-15N HSQC

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-99% 15N]		0.46 (±2.0E-5) mM
6	Sodium acetate	natural abundance		10.00 (±0.001) mM
7	H2O	natural abundance		90 (±0.001) mM
8	D2O	natural abundance		10 (±0.001) mM

7 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-99% 15N]		0.46 (±2.0E-5) mM
6	Sodium acetate	natural abundance		10.00 (±0.001) mM
7	H2O	natural abundance		90 (±0.001) mM
8	D2O	natural abundance		10 (±0.001) mM

8 2D 1H-15N HSQC

Instrument

Bruker Avance - 950 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.000 atm, Temperature 298.000 (±0.1) K, pH 5.300 (±0.1)

#	Name	Isotope labeling	Type	Concentration
5	entity	[U-99% 15N]		0.46 (±2.0E-5) mM
6	Sodium acetate	natural abundance		10.00 (±0.001) mM
7	H2O	natural abundance		90 (±0.001) mM
8	D2O	natural abundance		10 (±0.001) mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25251_2mv9.nef
Input source #2: Coordindates	2mv9.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:182:CYS:SG	A:217:CYS:SG	unknown, CA 58.46 ppm	unknown, CA 59.83 ppm	2.107

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
A	193	.	Not matched with CCD	None
A	196	.	Not matched with CCD	None
A	194	.	Not matched with CCD	None
A	195	.	Not matched with CCD	None

Sequence alignments

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

-------                                                                                             
....MGS                                                                                             
    |||                                                                                             
-.-.-G-SHHHHHHSSGLVPRGSHMSNKPSKPKTNMKHVAGAAAAGAVVGGLGGYMLGSVMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQN
 - - - ---------10--------20--------30--------40--------50--------60--------70--------80--------90--

                                                      
                                                      
                                                      
NFVHDCVNITVKQHTVKGENFTETDIKIMERVVEQMCITQYQRESQAYYQRGAS
-----100-------110-------120-------130-------140------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	150	4	0	100.0

Content subtype: combined_25251_2mv9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	Warning	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	958		89.6 (chain: A, length: 154)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1774 (1)	noe	83.8 (chain: A, length: 154)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	2 (1)	undefined	No information
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	142 (142)	.	55.8 (chain: A, length: 154)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 89.6%
- Total number of assignments
  - ¹³C chemical shifts: 138
  - ¹H chemical shifts: 674
  - ¹⁵N chemical shifts: 146
- Completeness of assignments
- Redox state of CYS
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: Warning

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 83.8%
- Total number of restraints: 1771
- Weight of restraints: 1.0 (1771)
- Potential type of restraints: upper-bound-parabolic (1771)
- Range of distance target values: 2.58, 6.39 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: undefined
  - Total number of restraints: 2
  - Weight of restraints: 1.0 (2)
  - Potential type of restraints: upper-bound-parabolic (2)
  - Range of distance target values: 3.0, 3.1 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 154, Sequence coverage: 55.8%
- Total number of restraints: 142
- Total number of restraints per polymer type: 142
- Weight of restraints: 1.0 (142)
- Potential type of restraints: square-well-parabolic (142)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords cellular form, deletion mutant, helix 2, major prion protein, prion, scrapie, transmissible spongiform encephalopathy