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Found 1 Document (1.55 seconds)

BMRB: 19062

2M5N

Atomic-resolution structure of a cross-beta protofilament

Authors

Fitzpatrick, A.W., Debelouchina, G.T., Bayro, M.J., Clare, D.K., Caporini, M.A., Bajaj, V.S., Jaroniec, C.P., Wang, L., Ladizhansky, V., Muller, S., MacPhee, C.E., Waudby, C.A., Mott, H.R., de Simone, A., Knowles, T.P., Saibil, H.R., Vendruscolo, M., Orlova, E.V., Griffin, R.G., Dobson, C.M.

Assembly

cross-beta protofilament

Entity

1. cross-beta protofilament (polymer, Thiol state: not present), 11 monomers, 1198.365 × 4 Da Detail

YTIAALLSPY S

Total weight

4793.46 Da

Max. entity weight

1198.365 Da

Source organism

Rattus norvegicus

Exptl. method

NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

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

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	100.0 % (63 of 63)	100.0 % (53 of 53)	100.0 % (10 of 10)
Backbone	100.0 % (43 of 43)	100.0 % (33 of 33)	100.0 % (10 of 10)
Sidechain	100.0 % (31 of 31)	100.0 % (31 of 31)
Aromatic	100.0 % (8 of 8)	100.0 % (8 of 8)
Methyl	100.0 % (9 of 9)	100.0 % (9 of 9)

1. protofilament part1

YTIAALLSPY S

Show sample condition

Sample

Solvent system 10% acetonitrile/water solution, Pressure 1 atm, Temperature 298 K, pH 2

#	Name	Isotope labeling	Concentration
1	TTR(105-115)	[U-100% 13C; U-100% 15N]	15 mg/mL
2	acetonitrile	natural abundance	10 %
3	H2O	natural abundance	90 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2M5N, Strand ID: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P Detail

Release date

2013-09-03

Citation

Atomic structure and hierarchical assembly of a cross-β amyloid fibril
Fitzpatrick, A.W.P., Debelouchina, G.T., Bayro, M.J., Clare, D.K., Caporini, M.A., Bajaj, V.S., Jaroniec, C.P., Wang, L., Ladizhansky, V., Muller, S.A., MacPhee, C.E., Waudby, C.A., Mott, H.R., De Simone, A., Knowles, T.P.J., Saibil, H.R., Vendruscolo, M., Orlova, E.V., Griffin, R.G., Dobson, C.M.
Proc. Natl. Acad. Sci. U. S. A. (2013), 110, 5468-5473, PubMed 23513222 , DOI 10.1073/pnas.1219476110 , Abstract

Related entities 1. cross-beta protofilament, : 1 : 105 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19062_2m5n.nef
Input source #2: Coordindates	2m5n.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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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YTIAALLSPYS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	11	100.0
B	B	11	100.0
C	C	11	100.0
D	D	11	100.0
E	E	11	100.0
F	F	11	100.0
G	G	11	100.0
H	H	11	100.0
I	I	11	100.0
J	J	11	100.0
K	K	11	100.0
L	L	11	100.0
M	M	11	100.0
A	A	11	100.0
A	A	11	100.0
A	A	11	100.0

Content subtype: combined_19062_2m5n.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	68		100.0 (chain: A, length: 11)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	868 (1)	noe	100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11), 100.0 (chain: C, length: 11), 100.0 (chain: D, length: 11), 100.0 (chain: E, length: 11), 100.0 (chain: F, length: 11), 100.0 (chain: G, length: 11), 100.0 (chain: H, length: 11), 100.0 (chain: I, length: 11), 100.0 (chain: J, length: 11), 100.0 (chain: K, length: 11), 100.0 (chain: L, length: 11), 100.0 (chain: M, length: 11), 100.0 (chain: N, length: 11), 100.0 (chain: O, length: 11), 100.0 (chain: P, length: 11)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	288 (288)	.	100.0 (chain: A, length: 11), 100.0 (chain: B, length: 11), 100.0 (chain: C, length: 11), 100.0 (chain: D, length: 11), 100.0 (chain: E, length: 11), 100.0 (chain: F, length: 11), 100.0 (chain: G, length: 11), 100.0 (chain: H, length: 11), 100.0 (chain: I, length: 11), 100.0 (chain: J, length: 11), 100.0 (chain: K, length: 11), 100.0 (chain: L, length: 11), 100.0 (chain: M, length: 11), 100.0 (chain: N, length: 11), 100.0 (chain: O, length: 11), 100.0 (chain: P, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 11, Sequence coverage: 100.0%
- Total number of assignments
  - ¹³C chemical shifts: 57
  - ¹⁵N chemical shifts: 11
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
1	TYR	CG	124.5
1	TYR	CZ	160.0
9	PRO	N	135.8
10	TYR	CG	128.7
10	TYR	CZ	157.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	53	53	100.0
¹⁵N chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	22	22	100.0
¹⁵N chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	31	31	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	9	9	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	8	8	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: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: E, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: F, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: G, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: H, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: I, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: J, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: K, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: L, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: M, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: N, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: O, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: P, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 868
- Weight of restraints: 1.0 (868)
- Potential type of restraints: square-well-parabolic (868)
- Range of distance target values: 2.3, 6.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
  - Chain_ID: F
  - Chain_ID: G
  - Chain_ID: H
  - Chain_ID: I
  - Chain_ID: J
  - Chain_ID: K
  - Chain_ID: L
  - Chain_ID: M
  - Chain_ID: N
  - Chain_ID: O
  - Chain_ID: P
- 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: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: D, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: E, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: F, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: G, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: H, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: I, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: J, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: K, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: L, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: M, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: N, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: O, Chain length: 11, Sequence coverage: 100.0%
  - Entity_assembly_ID: P, Chain length: 11, Sequence coverage: 100.0%
- Total number of restraints: 288
- Total number of restraints per polymer type: 288
- Weight of restraints: 1.0 (288)
- Potential type of restraints: square-well-parabolic (288)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C
  - Chain_ID: D
  - Chain_ID: E
  - Chain_ID: F
  - Chain_ID: G
  - Chain_ID: H
  - Chain_ID: I
  - Chain_ID: J
  - Chain_ID: K
  - Chain_ID: L
  - Chain_ID: M
  - Chain_ID: N
  - Chain_ID: O
  - Chain_ID: P

Keywords Amyloid fibril, Cross-beta structure

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Found 1 Document (1.55 seconds)

BMRB: 19062

Sample

Related entities 1. cross-beta protofilament, : 1 : 105 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail