BMRB Entry 36392

Name: Human RIPK3 amyloid fibril revealed by solid-state NMR
Published: 2025-09-15

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PDB ID: 7dac
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36392
MolProbity Validation Chart

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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:

Human RIPK3 amyloid fibril revealed by solid-state NMR

Deposition date:

2020-10-16

Original release date:

2025-09-15

Authors:

Wu, X.; Zhang, J.; Dong, X.; Liu, J.; Li, B.; Hu, H.; Wang, J.; Wang, H.; Lu, J.

Citation:

Citation: Wu, X.; Ma, Y.; Zhao, K.; Zhang, J.; Sun, Y.; Li, Y.; Dong, X.; Hu, H.; Liu, J.; Wang, J.; Zhang, X.; Li, B.; Wang, H.; Li, D.; Sun, B.; Lu, J.; Liu, C.. "The structure of a minimum amyloid fibril core formed by necroptosis-mediating RHIM of human RIPK3." Proc. Natl. Acad. Sci. U. S. A. 118, .-. (2021).
PubMed: 33790016

Assembly members:

Assembly members:
Receptor-interacting serine/threonine-protein kinase 3, polymer, 540 residues, 11863.072 Da.

Natural source:

Natural source: Common Name: human Taxonomy ID: 9606 Superkingdom: not available Kingdom: Metazoa Genus/species: Homo sapiens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Receptor-interacting serine/threonine-protein kinase 3: MHHHHHHSPGPRGNQGAERQ GMNWSCRTPEPNPVTGRPLV NIYNCSGVQVGDNNYLTMQQ TTALPTWGLAPSGKGRGLQH PPPVGSQEGPKDPEAWSRPQ GWYNHSGK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	111
15N chemical shifts	28

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

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
5	entity_1_5	1

Entities:

Entity 1, entity_1_1 540 residues - 11863.072 Da.

1

MET

HIS

SER

PRO

GLY

2

PRO

ARG

GLY

ASN

GLN

GLY

ALA

GLU

ARG

GLN

3

GLY

MET

ASN

TRP

SER

CYS

ARG

THR

PRO

GLU

4

PRO

ASN

PRO

VAL

THR

GLY

ARG

PRO

LEU

VAL

5

ASN

ILE

TYR

ASN

CYS

SER

GLY

VAL

GLN

VAL

6

GLY

ASP

ASN

TYR

LEU

THR

MET

GLN

7

THR

ALA

LEU

PRO

THR

TRP

GLY

LEU

ALA

8

PRO

SER

GLY

LYS

GLY

ARG

GLY

LEU

GLN

HIS

9

PRO

VAL

GLY

SER

GLN

GLU

GLY

PRO

10

LYS

ASP

PRO

GLU

ALA

TRP

SER

ARG

PRO

GLN

11

GLY

TRP

TYR

ASN

HIS

SER

GLY

LYS

Samples:

sample_1: human RIPK3 fibrils, [U-100% 13C; U-100% 15N], 5 ± 0.1 mg/mL; H2O 95%; D2O, [U-2H], 5%

sample_2: human RIPK3 fibrils, [U-100% 2-13C Glycerol; U-100% 15N], 5 ± 0.1 mg/mL; H2O 95%; D2O, [U-2H], 5%

sample_3: human RIPK3 fibrils, [U-100% 1, 3-13C Glycerol; U-100% 15N], 5 ± 0.5 mg/mL; H2O 95%; D2O, [U-2H], 5%

sample_4: human RIPK3 fibrils 5 ± 0.5 mg/mL; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 0 mM; pH: 7.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DARR 50ms mixing	sample_1	isotropic	sample_conditions_1
2D NcaCX 50ms mixing	sample_1	isotropic	sample_conditions_1
2D NcoCX 50ms mixing	sample_1	isotropic	sample_conditions_1
3D NCACX 50ms mixing	sample_1	isotropic	sample_conditions_1
3D NCOCX 50ms mixing	sample_1	isotropic	sample_conditions_1
2D DARR 50ms mixing	sample_2	isotropic	sample_conditions_1
2D DARR 200ms mixing	sample_2	isotropic	sample_conditions_1
2D DARR 500ms mixing	sample_2	isotropic	sample_conditions_1
2D DARR 50ms mixing	sample_3	isotropic	sample_conditions_1
2D DARR 200ms mixing	sample_3	isotropic	sample_conditions_1
2D DARR 500ms mixing	sample_3	isotropic	sample_conditions_1
2D DARR 50ms mixing	sample_4	isotropic	sample_conditions_1
2D DARR 200ms mixing	sample_4	isotropic	sample_conditions_1
2D DARR 500ms mixing	sample_4	isotropic	sample_conditions_1
2D DARR 200ms mixing	sample_1	isotropic	sample_conditions_1
2D DARR 500ms mixing	sample_1	isotropic	sample_conditions_1
zTEDOR 6.4ms mixing	sample_1	isotropic	sample_conditions_1
2D RFDR 10.7ms mixing	sample_1	isotropic	sample_conditions_1
zTEDOR 8.5ms mixing	sample_1	isotropic	sample_conditions_1
2D INEPT-TOBSY	sample_1	isotropic	sample_conditions_1
zTEDOR 6.4ms mixing	sample_2	isotropic	sample_conditions_1
zTEDOR 8.5ms mixing	sample_2	isotropic	sample_conditions_1
zTEDOR 6.4ms mixing	sample_3	isotropic	sample_conditions_1
zTEDOR 8.5ms mixing	sample_3	isotropic	sample_conditions_1
zTEDOR 6.4ms mixing	sample_4	isotropic	sample_conditions_1
zTEDOR 8.5ms mixing	sample_4	isotropic	sample_conditions_1
2D NHHC	sample_4	anisotropic	sample_conditions_1
2D DARR 50ms mixing	sample_1	isotropic	sample_conditions_1
2D DARR 200ms mixing	sample_1	isotropic	sample_conditions_1
2D DARR 500ms mixing	sample_1	isotropic	sample_conditions_1
2D NcaCX 50ms mixing	sample_1	isotropic	sample_conditions_1
2D NcoCX 50ms mixing	sample_1	isotropic	sample_conditions_1
3D NCACX 50ms mixing	sample_1	isotropic	sample_conditions_1
3D NCOCX 50ms mixing	sample_1	isotropic	sample_conditions_1
2D NcaCX 50ms mixing	sample_2	isotropic	sample_conditions_1
2D NcoCX 50ms mixing	sample_2	isotropic	sample_conditions_1
2D NcaCX 50ms mixing	sample_3	isotropic	sample_conditions_1
2D NcoCX 50ms mixing	sample_3	isotropic	sample_conditions_1

Software:

CNS, Brunger A. T. et.al. - refinement

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

Sparky, Goddard - chemical shift assignment

Sparky, Goddard - peak picking

NMR spectrometers:

Bruker AVANCE NEO 700 MHz
Agilent Direct Drive 700 MHz