BMRB Entry 34396
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34396
MolProbity Validation Chart
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NMR-STAR v3 text file.
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Title: Structure of pore-forming amyloid-beta tetramers PubMed: 32541820
Deposition date: 2019-04-23 Original release date: 2019-09-30
Authors: Bardiaux, B.; Ciudad, S.; Carulla, N.
Citation: Ciudad, Sonia; Puig, Eduard; Botzanowski, Thomas; Meigooni, Moeen; Arango, Andres; Do, Jimmy; Mayzel, Maxim; Bayoumi, Mariam; Chaignepain, Stephane; Maglia, Giovanni; Cianferani, Sarah; Orekhov, Vladislav; Tajkhorshid, Emad; Bardiaux, Benjamin; Carulla, Natalia. "Abeta(1-42) Tetramer and Octamer Structures Reveal Edge Conductivity Pores as a Mechanism for Membrane Damage" Nat. Commun. 11, 3014-3014 (2020).
Assembly members:
entity_1, polymer, 42 residues, 4520.087 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity_1: DAEFRHDSGYEVHHQKLVFF
AEDVGSNKGAIIGLMVGGVV
IA
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 368 |
| 15N chemical shifts | 132 |
| 1H chemical shifts | 132 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | entity_1, 1 | 1 |
| 2 | entity_1, 2 | 1 |
| 3 | entity_1, 3 | 1 |
| 4 | entity_1, 4 | 1 |
Entities:
Entity 1, entity_1, 1 42 residues - 4520.087 Da.
| 1 | ASP | ALA | GLU | PHE | ARG | HIS | ASP | SER | GLY | TYR | ||||
| 2 | GLU | VAL | HIS | HIS | GLN | LYS | LEU | VAL | PHE | PHE | ||||
| 3 | ALA | GLU | ASP | VAL | GLY | SER | ASN | LYS | GLY | ALA | ||||
| 4 | ILE | ILE | GLY | LEU | MET | VAL | GLY | GLY | VAL | VAL | ||||
| 5 | ILE | ALA |
Samples:
sample_1: Amyloid-beta A4 protein, [U-15N], 1 mM; TRIS-d11, [U-2H], 10 mM; DPC-d38, [U-2H], 28.5 mM
sample_2: Amyloid-beta A4 protein, [U-13C; U-15N; U-2H], 1 mM; TRIS-d11, [U-2H], 10 mM; DPC-d38, [U-2H], 28.5 mM
sample_3: Amyloid-beta A4 protein, [U-2H,13C,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR, 1 mM; TRIS-d11, [U-2H], 10 mM; DPC-d38, [U-2H], 28.5 mM
sample_4: Amyloid-beta A4 protein, [U-2H,15N]-Ile-[13CH3]d1, Ala-[13CH3], Leu/Val-[13CH3]proR, 1 mM; TRIS-d11, [U-2H], 10 mM; DPC-d38, [U-2H], 28.5 mM
sample_conditions_1: pH: 8.5; pressure: 1 atm; temperature: 310.15 K
sample_conditions_2: pH: 9.5; pressure: 1 atm; temperature: 310.15 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N TROSY | sample_1 | isotropic | sample_conditions_2 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_2 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_2 |
| 3D HN(COCA)CB | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C-HMQC-[1H,1H]-NOESY-13C-HMQC | sample_2 | isotropic | sample_conditions_1 |
| 3D (Hme)Cme([C]CA)CO | sample_3 | isotropic | sample_conditions_1 |
| 3D (Hme)Cme([C]CA)NH | sample_3 | isotropic | sample_conditions_1 |
| 3D Hme(Cme[C]CA)NH | sample_3 | isotropic | sample_conditions_1 |
| 3D (H)C-TOCSY-C-TOCSY-(C)H | sample_3 | isotropic | sample_conditions_1 |
| 3D Hm-CmHm NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D Cm-CmHm NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D Hm-NH NOESY | sample_4 | isotropic | sample_conditions_1 |
| 3D Cm-NH NOESY | sample_4 | isotropic | sample_conditions_1 |
| 2D 1H-15N TROSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D 13C-HMQC-[1H,1H]-NOESY-13C-HMQC | sample_2 | isotropic | sample_conditions_2 |
| 3D Hm-CmHm NOESY | sample_4 | isotropic | sample_conditions_2 |
| 3D Cm-CmHm NOESY | sample_4 | isotropic | sample_conditions_2 |
| 3D Hm-NH NOESY | sample_4 | isotropic | sample_conditions_2 |
| 3D Cm-NH NOESY | sample_4 | isotropic | sample_conditions_2 |
Software:
ARIA, Linge, O'Donoghue and Nilges - structure calculation
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
TALOS, Cornilescu, Delaglio and Bax - data analysis
TopSpin, Bruker Biospin - processing
CcpNmr Analysis, CCPN - chemical shift assignment
NMR spectrometers:
- Bruker AVANCE III 900 MHz
- Bruker AVANCE 800 MHz
Download HSQC peak lists in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts