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BMRB: 25558

2N1E

MAX1 peptide fibril

Authors

Nagy-Smith, K., Moore, E., Schneider, J., Tycko, R.

Assembly

MAX1 peptide fibril

Entity

1. MAX1 peptide fibril (polymer, Thiol state: not present), 21 monomers, 2228.907 × 8 Da Detail

VKVKVKVKVX PTKVKVKVKV X

Total weight

17831.256 Da

Max. entity weight

2228.907 Da

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 33.3 %, Completeness: 32.5 %, Completeness (bb): 32.0 % Detail

Polymer type: polypeptide(L)

	Total	¹³C	¹⁵N
All	32.5 % (39 of 120)	35.3 % (36 of 102)	16.7 % (3 of 18)
Backbone	32.0 % (24 of 75)	36.8 % (21 of 57)	16.7 % (3 of 18)
Sidechain	34.4 % (22 of 64)	34.4 % (22 of 64)
Methyl	36.8 % (7 of 19)	36.8 % (7 of 19)

1. MAX1

VKVKVKVKVX PTKVKVKVKV X

Protein Blocks Logo

Calculated from 20 models in PDB: 2N1E, Strand ID: A, B, C, D, E, F, G, H Detail

Release date

2015-07-26

Citation

Molecular-level Architecture of Self-Assembled Peptide Fibrils from Solid State NMR
Nagy-Smith, K., Moore, E., Schneider, J., Tycko, R.
Not known

Experiments performed 18 experiments Detail

1 REDOR

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

2 REDOR

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

3 REDOR

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

4 REDOR

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

5 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

6 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

7 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

8 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

9 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

10 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

11 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

12 PITHIRDS-CT

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

13 15N-BARE

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

14 13C-BARE

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

15 2D RAD/DARR

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

16 2D NCACX

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

17 2D RAD/DARR

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

18 2D NCACX

Instrument

#1 Model Varian InfinityPlus (400 MHz)

#2 Model Bruker Avance III (400 MHz)

#3 Model Varian Infinity (750 MHz)

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25558_2n1e.nef
Input source #2: Coordindates	2n1e.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:9:VAL:C	1:10:DPR:N	unknown	unknown	n/a
1:10:DPR:C	1:11:PRO:N	unknown	unknown	n/a
1:20:VAL:C	1:21:NH2:N	unknown	unknown	n/a
2:9:VAL:C	2:10:DPR:N	unknown	unknown	n/a
2:10:DPR:C	2:11:PRO:N	unknown	unknown	n/a
2:20:VAL:C	2:21:NH2:N	unknown	unknown	n/a
3:9:VAL:C	3:10:DPR:N	unknown	unknown	n/a
3:10:DPR:C	3:11:PRO:N	unknown	unknown	n/a
3:20:VAL:C	3:21:NH2:N	unknown	unknown	n/a
4:9:VAL:C	4:10:DPR:N	unknown	unknown	n/a
4:10:DPR:C	4:11:PRO:N	unknown	unknown	n/a
4:20:VAL:C	4:21:NH2:N	unknown	unknown	n/a
5:9:VAL:C	5:10:DPR:N	unknown	unknown	n/a
5:10:DPR:C	5:11:PRO:N	unknown	unknown	n/a
5:20:VAL:C	5:21:NH2:N	unknown	unknown	n/a
6:9:VAL:C	6:10:DPR:N	unknown	unknown	n/a
6:10:DPR:C	6:11:PRO:N	unknown	unknown	n/a
6:20:VAL:C	6:21:NH2:N	unknown	unknown	n/a
7:9:VAL:C	7:10:DPR:N	unknown	unknown	n/a
7:10:DPR:C	7:11:PRO:N	unknown	unknown	n/a
7:20:VAL:C	7:21:NH2:N	unknown	unknown	n/a
8:9:VAL:C	8:10:DPR:N	unknown	unknown	n/a
8:10:DPR:C	8:11:PRO:N	unknown	unknown	n/a
8:20:VAL:C	8:21:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	10	DPR	D-PROLINE	Assigned chemical shifts, Torsion angle restraints, Coordinates
A	21	NH2	AMINO GROUP	Coordinates
B	10	DPR	D-PROLINE	Coordinates
B	21	NH2	AMINO GROUP	Coordinates
C	10	DPR	D-PROLINE	Coordinates
C	21	NH2	AMINO GROUP	Coordinates
D	10	DPR	D-PROLINE	Coordinates
D	21	NH2	AMINO GROUP	Coordinates
E	10	DPR	D-PROLINE	Coordinates
E	21	NH2	AMINO GROUP	Coordinates
F	10	DPR	D-PROLINE	Coordinates
F	21	NH2	AMINO GROUP	Coordinates
G	10	DPR	D-PROLINE	Coordinates
G	21	NH2	AMINO GROUP	Coordinates
H	10	DPR	D-PROLINE	Coordinates
H	21	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

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

--------10--------20-
VKVKVKVKVXPTKVKVKVKVX
|||||||||||||||||||||
VKVKVKVKVXPTKVKVKVKVX

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	21	0	0	100.0
B	B	21	0	0	100.0
C	C	21	0	0	100.0
D	D	21	0	0	100.0
E	E	21	0	0	100.0
F	F	21	0	0	100.0
G	G	21	0	0	100.0
H	H	21	0	0	100.0

Content subtype: combined_25558_2n1e.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	24		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	41		38.1 (chain: A, length: 21)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	75 (1)	noe	76.2 (chain: A, length: 21), 81.0 (chain: B, length: 21), 81.0 (chain: C, length: 21), 61.9 (chain: D, length: 21), 61.9 (chain: E, length: 21), 81.0 (chain: F, length: 21), 81.0 (chain: G, length: 21), 61.9 (chain: H, length: 21)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	33 (33)	.	95.2 (chain: A, length: 21)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 38.1%
- Total number of assignments
  - ¹³C chemical shifts: 37
  - ¹⁵N chemical shifts: 4
- Completeness of assignments
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 21, Sequence coverage: 76.2%
  - Entity_assembly_ID: B, Chain length: 21, Sequence coverage: 81.0%
  - Entity_assembly_ID: C, Chain length: 21, Sequence coverage: 81.0%
  - Entity_assembly_ID: D, Chain length: 21, Sequence coverage: 61.9%
  - Entity_assembly_ID: E, Chain length: 21, Sequence coverage: 61.9%
  - Entity_assembly_ID: F, Chain length: 21, Sequence coverage: 81.0%
  - Entity_assembly_ID: G, Chain length: 21, Sequence coverage: 81.0%
  - Entity_assembly_ID: H, Chain length: 21, Sequence coverage: 61.9%
- Total number of restraints: 75
- Weight of restraints: 1.0 (75)
- Potential type of restraints: square-well-parabolic (75)
- Range of distance target values: 2.67, 4.5 (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
- 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: 21, Sequence coverage: 95.2%
- Total number of restraints: 33
- Total number of restraints per polymer type: 33
- Weight of restraints: 1.0 (33)
- Potential type of restraints: square-well-parabolic (33)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords amyloid-like, biomaterials, cross-beta, designed peptide, hydrogel