BMRBj - BMREntryMaster

Found 1 Document (1.221 seconds)

BMRB: 19268

2M8T

SOLUTION NMR STRUCTURE OF THE V209M VARIANT OF THE HUMAN PRION PROTEIN (RESIDUES 90-231)

Authors

Mills, J.L., Surewicz, K., Surewicz, W., Soennichsen, F.D.

Assembly

HuPRP

Entity

1. HuPRP (polymer, Thiol state: all disulfide bound), 146 monomers, 16536.21 Da Detail

GSDPGQGGGT HSQWNKPSKP KTNMKHMAGA AAAGAVVGGL GGYMLGSAMS RPIIHFGSDY EDRYYRENMH RYPNQVYYRP MDEYSNQNNF VHDCVNITIK QHTVTTTTKG ENFTETDVKM MERMVEQMCI TQYERESQAY YQRGSS

Formula weight

16536.21 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics, MOLECULAR DYNAMICS

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 84.5 %, Completeness (bb): 81.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.5 % (1404 of 1662)	91.9 % (799 of 869)	71.5 % (453 of 634)	95.6 % (152 of 159)
Backbone	81.7 % (706 of 864)	93.4 % (281 of 301)	69.0 % (292 of 423)	95.0 % (133 of 140)
Sidechain	88.6 % (823 of 929)	91.2 % (518 of 568)	83.6 % (286 of 342)	100.0 % (19 of 19)
Aromatic	64.9 % (100 of 154)	87.0 % (67 of 77)	42.1 % (32 of 76)	100.0 % (1 of 1)
Methyl	98.0 % (96 of 98)	98.0 % (48 of 49)	98.0 % (48 of 49)

1. MAJOR PRION PROTEIN

GSDPGQGGGT HSQWNKPSKP KTNMKHMAGA AAAGAVVGGL GGYMLGSAMS RPIIHFGSDY EDRYYRENMH RYPNQVYYRP MDEYSNQNNF VHDCVNITIK QHTVTTTTKG ENFTETDVKM MERMVEQMCI TQYERESQAY YQRGSS

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-5% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
6	MAJOR PRION PROTEIN	[U-5% 13C; U-99% 15N]	1.0 mM
7	sodium acetate	natural abundance	10 mM
8	sodium azide	natural abundance	0.005 w/v
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.04 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M8T, Strand ID: A Detail

Release date

2013-09-09

Citation

Thermodynamic stabilization of the folded domain of prion protein inhibits prion infection in vivo
Kong, Q., Mills, J.L., Kundu, B., Li, X., Qing, L., Surewicz, K., Cali, I., Huang, S., Zheng, M., Swietnicki, W., Soennichsen, F.D., Gambetti, P., Surewicz, W.K.
Cell Rep. (2013), 4, 248-254, PubMed 23871665 , DOI 10.1016/j.celrep.2013.06.030 , Abstract

Related entities 1. HuPRP, : 1 : 1 : 99 entities Detail

Interaction partners 1. HuPRP, : 73 interactors Detail

More details for 73 interactors identified by 15 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

2 2D 1H-13C HSQC ALIPHATIC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

3 2D 1H-13C HSQC AROMATIC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

4 2D 1H-1H NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

5 3D HNCA

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

6 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

7 3D C(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

8 3D HCCH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

9 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

10 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

11 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-5% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
6	MAJOR PRION PROTEIN	[U-5% 13C; U-99% 15N]	1.0 mM
7	sodium acetate	natural abundance	10 mM
8	sodium azide	natural abundance	0.005 w/v
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %

12 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

13 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

14 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

15 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 299 K, pH 4.6, Details 1.0 MM [U-99% 13C, U-99% 15N]

#	Name	Isotope labeling	Concentration
1	MAJOR PRION PROTEIN	[U-99% 13C; U-99% 15N]	1.0 mM
2	sodium acetate	natural abundance	10 mM
3	sodium azide	natural abundance	0.005 w/v
4	H2O	natural abundance	95 %
5	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19268_2m8t.nef
Input source #2: Coordindates	2m8t.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

---90-------100-------110-------120-------130-------140-------150-------160-------170-------180-----
GSDPGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSDPGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--190-------200-------210-------220-------230-
QHTVTTTTKGENFTETDVKMMERMVEQMCITQYERESQAYYQRGSS
||||||||||||||||||||||||||||||||||||||||||||||
QHTVTTTTKGENFTETDVKMMERMVEQMCITQYERESQAYYQRGSS
-------110-------120-------130-------140------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	146	0	0	100.0

Content subtype: combined_19268_2m8t.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1385		98.6 (chain: A, length: 146)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1884 (1)	noe	73.3 (chain: A, length: 146)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	124 (124)	.	50.0 (chain: A, length: 146)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 146, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 800
  - ¹³C chemical shifts: 425
  - ¹⁵N chemical shifts: 160
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	869	800	92.1
¹³C chemical shifts	634	425	67.0
¹⁵N chemical shifts	167	160	95.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	301	284	94.4
¹³C chemical shifts	292	142	48.6
¹⁵N chemical shifts	140	133	95.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	568	516	90.8
¹³C chemical shifts	342	283	82.7
¹⁵N chemical shifts	27	27	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	59	100.0
¹³C chemical shifts	59	59	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	77	67	87.0
¹³C chemical shifts	76	32	42.1
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 146, Sequence coverage: 73.3%
- Total number of restraints: 1879
- Weight of restraints: 1.0 (1879)
- Potential type of restraints: square-well-parabolic (1879)
- Range of distance target values: 1.12, 2.75 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 146, Sequence coverage: 50.0%
- Total number of restraints: 124
- Total number of restraints per polymer type: 124
- Weight of restraints: 1.0 (124)
- Potential type of restraints: square-well-parabolic (124)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HUMAN, MEMBRANE PROTEIN, PRION

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (1.221 seconds)

BMRB: 19268

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HuPRP, : 1 : 1 : 99 entities Detail

Interaction partners 1. HuPRP, : 73 interactors Detail

Experiments performed 15 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail