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Found 1 Document (0.636 seconds)

BMRB: 19157

3ZPK

ATOMIC-RESOLUTION STRUCTURE OF A CROSS-BETA QUADRUPLET AMYLOID FIBRIL DETERMINED BY SOLID-STATE MAGIC ANGLE SPINNING NMR AND CRYO-EM

Authors

Fitzpatrick, A.WILLIAM., 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.J., Saibil, H.R., Vendruscolo, M., Orlova, E.V., Griffin, R.G., Dobson, C.M., Bajaj, M., De-simone, A.

Assembly

Atomic-resolution structure of a quadruplet cross-beta amyloid fibril

Entity

1. Atomic-resolution structure of a quadruplet cross-beta amyloid fibril (polymer, Thiol state: not present), 11 monomers, 1198.365 × 48 Da Detail

YTIAALLSPY S

Total weight

57521.52 Da

Max. entity weight

1198.365 Da

Exptl. method

NMR

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 88.9 %, Completeness (bb): 93.0 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	88.9 % (56 of 63)	90.6 % (48 of 53)	80.0 % (8 of 10)
Backbone	93.0 % (40 of 43)	97.0 % (32 of 33)	80.0 % (8 of 10)
Sidechain	83.9 % (26 of 31)	83.9 % (26 of 31)
Aromatic	50.0 % (4 of 8)	50.0 % (4 of 8)
Methyl	100.0 % (9 of 9)	100.0 % (9 of 9)

1. TRANSTHYRETIN (chain A)

YTIAALLSPY S

Show sample condition

Sample

Solvent system 10% V/V ACETONITRILE/WATER, Pressure 1.000 atm, Temperature 288.150 K, Details n/a

#	Name	Isotope labeling	Type	Concentration
1	TRANSTHYRETIN (chain A)	natural abundance		na mM

Protein Blocks Logo

Calculated from 1 models in PDB: 3ZPK, Strand ID: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P Detail

Release date

2013-04-09

Citation

Atomic structure and hierarchical assembly of a cross-β amyloid fibril
Fitzpatrick, A.WILLIAM., 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.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

Entries sharing articles BMRB: 3, EMDB: 3 entries Detail

  BMRB: 19058 released on 2013-10-29
    Title Atomic-resolution structure of a doublet cross-beta amyloid fibril
  BMRB: 19060 released on 2013-10-29
    Title Atomic-resolution structure of a triplet cross-beta amyloid fibril
  BMRB: 19062 released on 2013-09-03
    Title Atomic-resolution structure of a cross-beta protofilament
  EMDB: 5590 released on 2013-04-03
    Title Electron cryo-microscopy of a cross-beta amyloid fibril polymorph
  EMDB: 2323 released on 2013-03-27
    Title Electron cryo-microscopy of a cross-beta amyloid fibril polymorph
  EMDB: 2324 released on 2013-03-27
    Title Electron cryo-microscopy of a cross-beta amyloid fibril polymorph

Related entities 1. Atomic-resolution structure of a quadruplet cross-beta amyloid fibril, : 1 : 105 entities Detail

Experiments performed 6 experiments Detail

NMR combined restraints 2 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts	combined_19157_3zpk.nef
Input source #2: Coordindates	3zpk.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	Error

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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YTIAALLSPYS

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

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YTIAALLSPYS

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

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YTIAALLSPYS

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

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YTIAALLSPYS

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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YTIAALLSPYS

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

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YTIAALLSPYS

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

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YTIAALLSPYS

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

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YTIAALLSPYS

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

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YTIAALLSPYS

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

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YTIAALLSPYS

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

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YTIAALLSPYS

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_19157_3zpk.nef

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list	Warning	62		100.0 (chain: A, length: 11)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list
- 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: 52
  - ¹⁵N chemical shifts: 10
- 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	48	90.6
¹⁵N chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	22	22	100.0
¹⁵N chemical shifts	10	9	90.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	31	26	83.9

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	4	50.0

Keywords Amyloid, PROTEIN FIBRIL, cross-beta structure, polymorphism

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Found 1 Document (0.636 seconds)

BMRB: 19157

Sample

Entries sharing articles BMRB: 3, EMDB: 3 entries Detail

Related entities 1. Atomic-resolution structure of a quadruplet cross-beta amyloid fibril, : 1 : 105 entities Detail

Experiments performed 6 experiments Detail

Instrument

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NMR combined restraints 2 contents Detail