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Found 1 Document (1.155 seconds)

BMRB: 11028

2KJ3

Solid-state NMR assignment of the rigid core of the HET-s(218-289) prion protein in its amyloid conformation.

Authors

Siemer, A., Wasmer, C., Lange, A., Van Melckebeke, H., Ernst, M., Ritter, C.H., Steinmetz, M.O., Riek, R., Meier, B.H.

Assembly

HET-s(218-289)

Entity

1. HET-s(218-289) (polymer, Thiol state: not present), 79 monomers, 8650.510 Da Detail

MKIDAIVGRN SAKDIRTEER ARVQLGNVVT AAALHGGIRI SDQTTNSVET VVGKGESRVL IGNEYGGKGF WDNHHHHHH

Formula weight

8650.51 Da

Source organism

Podospora anserina

Exptl. method

solid-state NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 63.3 %, Completeness: 62.9 %, Completeness (bb): 63.7 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	62.9 % (266 of 423)	62.8 % (211 of 336)	63.2 % (55 of 87)
Backbone	63.7 % (195 of 306)	63.9 % (145 of 227)	63.3 % (50 of 79)
Sidechain	62.4 % (116 of 186)	62.4 % (111 of 178)	62.5 % (5 of 8)
Aromatic	51.7 % (15 of 29)	50.0 % (14 of 28)	100.0 % (1 of 1)
Methyl	73.3 % (33 of 45)	73.3 % (33 of 45)

1. HET-s(218-289)

MKIDAIVGRN SAKDIRTEER ARVQLGNVVT AAALHGGIRI SDQTTNSVET VVGKGESRVL IGNEYGGKGF WDNHHHHHH

Show sample condition

Sample

Pressure 1 atm, Temperature 278 (±2) K, pH 7.5, Details "Wet" fibrils sample: the total amount of water in the sample is at least 60% (weight). Below, the concentration is given with respect to the total protein concentration.

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantan	methine carbon	31.47 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.32 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantan	methine carbon	31.47 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: -0.32 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	adamantan	methine carbon	31.47 ppm	external	direct	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	null	indirect	0.1013291

Referencing offset: 0.84 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2RNM, Strand ID: A, B, C, D, E Detail

Release date

2009-03-30

Citation 1

Amyloid fibrils of the HET-s(218-289) prion form a beta solenoid with a triangular hydrophobic core
Wasmer, C., Lange, A., Van Melckebeke, H., Siemer, A., Riek, R., Meier, B.H.
Science (2008), 319, 1523-1526, PubMed 18339938 , DOI 10.1126/science.1151839 , Abstract

Show more 1 citaion

Citation 2

13C, 15N resonance assignment of parts of the HET-s prion protein in its amyloid form
Siemer, A., Ritter, C., Steinmetz, M.O., Ernst, M., Riek, R., Meier, B.H.
J. Biomol. NMR (2006), 34, 75-87, PubMed 16518695 , DOI 10.1007/s10858-005-5582-7 , Abstract

Hide non-primary 1 citaion

Related entities 1. HET-s(218-289), : 1 : 2 : 1 : 1 : 2 entities Detail

Interaction partners 1. HET-s(218-289), : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 9 experiments Detail

1 DREAM

Instrument

Bruker Avance - 600 MHz

Sample

State solid, Pressure 1 atm, Temperature 278 (±2) K, pH 7.5, Details "Wet" fibrils sample: the total amount of water in the sample is at least 60% (weight). Below, the concentration is given with respect to the total protein concentration.

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

2 TOBSY

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

3 PDSD

Instrument

Bruker Avance - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

4 NCA

Instrument

Bruker Avance - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

5 NCO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

6 N(CO)CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

7 N(CO)CB

Instrument

Bruker Avance - 850 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

8 N(CA)CO

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

9 CA-CA

Instrument

Bruker Avance - 600 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	HET-s(218-289)	[U-100% 13C; U-100% 15N]	protein	5.0 ~ 40.0 mg
2	H2O	natural abundance		7.5 ~ 0.0 %

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr11028_3.str
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

Content subtype: bmr11028_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	273		60.8 (chain: 1, length: 79)
1	Chemical shift references	chemical_shift_reference_1	Warning	2		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: 1, Chain length: 79, Sequence coverage: 60.8%

--------10--------20--------30--------40--------50--------60--------70---------
MKIDAIVGRNSAKDIRTEERARVQLGNVVTAAALHGGIRISDQTTNSVETVVGKGESRVLIGNEYGGKGFWDNHHHHHH
         |||||||||||||||||||||||           |||||||||||||||||||||||   ||        
.........NSAKDIRTEERARVQLGNVVTAA...........TTNSVETVVGKGESRVLIGNEYG...FW        
--------10--------20--------30--------40--------50--------60--------70-

Total number of assignments
- ¹³C chemical shifts: 217
- ¹⁵N chemical shifts: 56

Completeness of assignments

Entity_assemble_ID: 1

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	ASN	CG	177.4
14	ASP	CG	179.7
18	GLU	CD	182.9
19	GLU	CD	184.8
24	GLN	CD	175.7
27	ASN	CG	176.1
46	ASN	CG	176.5
49	GLU	CD	183.6
54	LYS	NZ	33.9
56	GLU	CD	184.9
63	ASN	CG	176.3
64	GLU	CD	181.8
65	TYR	CG	127.6
70	PHE	CG	136.5
71	TRP	CG	112.1
71	TRP	CD2	129.3

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	336	202	60.1
¹⁵N chemical shifts	93	55	59.1

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	158	96	60.8
¹⁵N chemical shifts	79	48	60.8

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	178	106	59.6
¹⁵N chemical shifts	14	7	50.0

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	46	31	67.4

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	28	14	50.0
¹⁵N chemical shifts	1	1	100.0

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: 1

Keywords amyloid fibril, asparagine ladders, beta-helix, beta-solenoid, HET-s(218-289), hydrophobic core, parallel beta-sheets, prion, salt bridges

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Found 1 Document (1.155 seconds)

BMRB: 11028

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. HET-s(218-289), : 1 : 2 : 1 : 1 : 2 entities Detail

Interaction partners 1. HET-s(218-289), : 1 interactors Detail

Experiments performed 9 experiments Detail

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Chemical shift validation 3 contents Detail