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BMRB: 16505

2KKG

NMR structure of the octarepeat region of prion protein bound to pentosan polysulfate

Authors

Taubner, L.M., Caughey, B., Copie, V.

Assembly

octarepeats

Entity

1. octarepeats (polymer, Thiol state: not present), 85 monomers, 8682.273 Da Detail

MKKRPKPGGW NTGGSRYPGQ GSPGGNRYPP QGGGTWGQPH GGGWGQPHGG GWGQPHGGGW GQPHGGGWGQ GGGTHNQWNK PSKPK

Formula weight

8682.273 Da

Source organism

Mesocricetus auratus

Exptl. method

solution NMR

Refine. method

simulated annealing, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 81.2 %, Completeness: 53.1 %, Completeness (bb): 62.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	53.1 % (493 of 929)	53.5 % (267 of 499)	50.9 % (172 of 338)	58.7 % (54 of 92)
Backbone	62.3 % (303 of 486)	64.6 % (122 of 189)	56.7 % (127 of 224)	74.0 % (54 of 73)
Sidechain	48.3 % (240 of 497)	46.8 % (145 of 310)	56.5 % (95 of 168)	0.0 % (0 of 19)
Aromatic	10.0 % (12 of 120)	20.0 % (12 of 60)	0.0 % (0 of 53)	0.0 % (0 of 7)
Methyl	100.0 % (6 of 6)	100.0 % (3 of 3)	100.0 % (3 of 3)

1. octarepeats

MKKRPKPGGW NTGGSRYPGQ GSPGGNRYPP QGGGTWGQPH GGGWGQPHGG GWGQPHGGGW GQPHGGGWGQ GGGTHNQWNK PSKPK

Show sample condition

Sample #1

Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
1	octarepeats	[U-15N]	0.5 mM
2	D2O	[U-2H]	5 %
3	DMSO	[U-2H]	20 %
4	pentosan polysulfate	natural abundance	20 mM
5	sodium acetate	natural abundance	10 mM
6	H2O	natural abundance	75 %

Sample #2

Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
7	octarepeats	[U-13C; U-15N]	0.5 mM
8	D2O	[U-2H]	5 %
9	DMSO	[U-2H]	20 %
10	pentosan polysulfate	natural abundance	20 mM
11	sodium acetate	natural abundance	10 mM
12	H2O	natural abundance	75 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate

#	Name	Isotope labeling	Concentration
13	octarepeats	[U-13C; U-15N]	0.5 mM
14	D2O	[U-2H]	80 %
15	DMSO	[U-2H]	20 %
16	pentosan polysulfate	natural abundance	20 mM
17	sodium acetate	natural abundance	10 mM

LACS Plot; CA

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

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.02 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2009-11-19

Citation

Structure of the flexible amino-terminal domain of prion protein bound to a sulfated glycan
Taubner, L.M., Bienkiewicz, E.A., Copie, V., Caughey, B.
J. Mol. Biol. (2010), 395, 475-490, PubMed 19913031 , DOI 10.1016/j.jmb.2009.10.075 , Abstract

Related entities 1. octarepeats, : 1 : 4 : 51 entities Detail

Interaction partners 1. octarepeats, : 2 interactors Detail

More details for 2 interactors identified by 2 citations

Experiments performed 11 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
1	octarepeats	[U-15N]	0.5 mM
2	D2O	[U-2H]	5 %
3	DMSO	[U-2H]	20 %
4	pentosan polysulfate	natural abundance	20 mM
5	sodium acetate	natural abundance	10 mM
6	H2O	natural abundance	75 %

2 2D 1H-13C HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate

#	Name	Isotope labeling	Concentration
13	octarepeats	[U-13C; U-15N]	0.5 mM
14	D2O	[U-2H]	80 %
15	DMSO	[U-2H]	20 %
16	pentosan polysulfate	natural abundance	20 mM
17	sodium acetate	natural abundance	10 mM

3 3D CBCA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
7	octarepeats	[U-13C; U-15N]	0.5 mM
8	D2O	[U-2H]	5 %
9	DMSO	[U-2H]	20 %
10	pentosan polysulfate	natural abundance	20 mM
11	sodium acetate	natural abundance	10 mM
12	H2O	natural abundance	75 %

4 3D C(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
7	octarepeats	[U-13C; U-15N]	0.5 mM
8	D2O	[U-2H]	5 %
9	DMSO	[U-2H]	20 %
10	pentosan polysulfate	natural abundance	20 mM
11	sodium acetate	natural abundance	10 mM
12	H2O	natural abundance	75 %

5 3D HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
7	octarepeats	[U-13C; U-15N]	0.5 mM
8	D2O	[U-2H]	5 %
9	DMSO	[U-2H]	20 %
10	pentosan polysulfate	natural abundance	20 mM
11	sodium acetate	natural abundance	10 mM
12	H2O	natural abundance	75 %

6 3D HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
7	octarepeats	[U-13C; U-15N]	0.5 mM
8	D2O	[U-2H]	5 %
9	DMSO	[U-2H]	20 %
10	pentosan polysulfate	natural abundance	20 mM
11	sodium acetate	natural abundance	10 mM
12	H2O	natural abundance	75 %

7 3D HBHA(CO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
7	octarepeats	[U-13C; U-15N]	0.5 mM
8	D2O	[U-2H]	5 %
9	DMSO	[U-2H]	20 %
10	pentosan polysulfate	natural abundance	20 mM
11	sodium acetate	natural abundance	10 mM
12	H2O	natural abundance	75 %

8 3D H(CCO)NH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
7	octarepeats	[U-13C; U-15N]	0.5 mM
8	D2O	[U-2H]	5 %
9	DMSO	[U-2H]	20 %
10	pentosan polysulfate	natural abundance	20 mM
11	sodium acetate	natural abundance	10 mM
12	H2O	natural abundance	75 %

9 3D HCCH-TOCSY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate

#	Name	Isotope labeling	Concentration
13	octarepeats	[U-13C; U-15N]	0.5 mM
14	D2O	[U-2H]	80 %
15	DMSO	[U-2H]	20 %
16	pentosan polysulfate	natural abundance	20 mM
17	sodium acetate	natural abundance	10 mM

10 3D 1H-15N NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 75% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate pH=5.0

#	Name	Isotope labeling	Concentration
1	octarepeats	[U-15N]	0.5 mM
2	D2O	[U-2H]	5 %
3	DMSO	[U-2H]	20 %
4	pentosan polysulfate	natural abundance	20 mM
5	sodium acetate	natural abundance	10 mM
6	H2O	natural abundance	75 %

11 3D 1H-13C NOESY

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 5.0, Details 20% DMSO final volume 40 X excess pentosan polysulfate

#	Name	Isotope labeling	Concentration
13	octarepeats	[U-13C; U-15N]	0.5 mM
14	D2O	[U-2H]	80 %
15	DMSO	[U-2H]	20 %
16	pentosan polysulfate	natural abundance	20 mM
17	sodium acetate	natural abundance	10 mM

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16505_2kkg.nef
Input source #2: Coordindates	2kkg.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

-------30--------40--------50--------60--------70--------80--------90-------100------
MKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGTWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHNQWNKPSKPK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGTWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHNQWNKPSKPK
--------10--------20--------30--------40--------50--------60--------70--------80-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	85	0	0	100.0

Content subtype: combined_16505_2kkg.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	465		77.6 (chain: A, length: 85)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	538 (1)	noe	36.5 (chain: A, length: 85)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 85, Sequence coverage: 77.6%
- Total number of assignments
  - ¹H chemical shifts: 255
  - ¹³C chemical shifts: 160
  - ¹⁵N chemical shifts: 50
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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	499	255	51.1
¹³C chemical shifts	338	160	47.3
¹⁵N chemical shifts	95	50	52.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	189	110	58.2
¹³C chemical shifts	170	66	38.8
¹⁵N chemical shifts	73	50	68.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	310	145	46.8
¹³C chemical shifts	168	94	56.0
¹⁵N chemical shifts	22	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	3	75.0
¹³C chemical shifts	4	3	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	60	12	20.0
¹³C chemical shifts	53	0	0.0
¹⁵N chemical shifts	7	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: 85, Sequence coverage: 36.5%
- Total number of restraints: 538
- Weight of restraints: 1.0 (538)
- Potential type of restraints: square-well-parabolic (538)
- Range of distance target values: 2.4, 3.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords nmr, octapeptide repeats, pentosan polysulfate, prion protein, sulfated glycans

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Found 1 Document (0.817 seconds)

BMRB: 16505

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. octarepeats, : 1 : 4 : 51 entities Detail

Interaction partners 1. octarepeats, : 2 interactors Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 3 contents Detail