BMRB Entry 34396

Name: Structure of pore-forming amyloid-beta tetramers
Published: 2019-09-30

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PDB ID: 6rhy
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34396
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Structure of pore-forming amyloid-beta tetramers

Deposition date:

2019-04-23

Original release date:

2019-09-30

Authors:

Bardiaux, B.; Ciudad, S.; Carulla, N.

Citation:

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).
PubMed: 32541820

Assembly members:

Assembly members:
entity_1, polymer, 42 residues, 4520.087 Da.

Natural source:

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: DAEFRHDSGYEVHHQKLVFF AEDVGSNKGAIIGLMVGGVV IA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	368
15N chemical shifts	132
1H chemical shifts	132

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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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

GLN

LYS

LEU

VAL

PHE

3

ALA

GLU

ASP

VAL

GLY

SER

ASN

LYS

GLY

ALA

4

ILE

GLY

LEU

MET

VAL

GLY

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 peaks
SPARKY: Backbone or all simulated peaks