BMRB Entry 34971

Name: SSNMR structure of amyloid fibrils formed by human RIPK1
Published: 2025-09-17

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PDB ID: 9hr9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34971
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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:

SSNMR structure of amyloid fibrils formed by human RIPK1

Deposition date:

2024-12-17

Original release date:

2025-09-17

Authors:

Polonio, P.; Escobedo-Gonzales, F.; Titaux-Delgado, G.; Mompean, M.

Citation:

Citation: Polonio, P.; Lopez-Alonso, J.; Ubarretxena-Belandia, I.; Jiang, H.; Escobedo-Gonzales, F.; Titaux-Delgado, G.; Mompean, M.. "Molecular Structure of Human Receptor Interacting Protein Kinase 1 (RIPK1) in its Fibrillar Conformation Elucidated by Solid-State NMR and Cryo-Electron Microscopy" .

Assembly members:

Assembly members:
entity_1, polymer, 22 residues, 2513.842 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 BL21(DE3) Vector: pET11a

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: IKYTIYNSTGIQIGAYNYME IG

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	98
15N chemical shifts	18

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 22 residues - 2513.842 Da.

1

ILE

LYS

TYR

THR

ILE

TYR

ASN

SER

THR

GLY

2

ILE

GLN

ILE

GLY

ALA

TYR

ASN

TYR

MET

GLU

3

ILE

GLY

Samples:

sample_1: protein, [U-100% 13C; U-100% 15N], 25 % w/w

sample_conditions_1: ionic strength: 0 mM; pH: 7.4; pressure: 1 atm; temperature: 310 K

Experiments:

Name	Sample	Sample state	Sample conditions
NCACX	sample_1	isotropic	sample_conditions_1
NCOCX	sample_1	isotropic	sample_conditions_1
CANCOCX	sample_1	isotropic	sample_conditions_1
CORD 20 ms	sample_1	isotropic	sample_conditions_1
CORD 50 ms	sample_1	isotropic	sample_conditions_1
CORD 100 ms	sample_1	isotropic	sample_conditions_1
CORD 500 ms	sample_1	isotropic	sample_conditions_1

Software:

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

GROMACS, https://doi.org/10.5281/zenodo.11148638 - refinement

CcpNmr Analysis, CCPN - chemical shift assignment

NMR spectrometers:

Bruker AVANCE NEO 600 MHz