BMRB Entry 36243

Name: Mouse receptor-interacting protein kinase 3 (RIP3) amyloid structure by solid-state NMR
Published: 2023-02-23

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PDB ID: 6jpd
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36243
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:

Mouse receptor-interacting protein kinase 3 (RIP3) amyloid structure by solid-state NMR

Deposition date:

2019-03-26

Original release date:

2023-02-23

Authors:

Wu, X.; Hu, H.; Zhang, J.; Dong, X.; Wang, J.; Schwieters, C.; Wang, H.; Lu, J.

Citation:

Citation: Wu, Xia-Lian; Hu, Hong; Dong, Xing-Qi; Zhang, Jing; Wang, Jian; Schwieters, Charles; Liu, Jing; Wu, Guo-Xiang; Li, Bing; Lin, Jing-Yu; Wang, Hua-Yi; Lu, Jun-Xia. "The amyloid structure of mouse RIPK3 (receptor interacting protein kinase 3) in cell necroptosis." Nat. Commun. 12, 1627-1627 (2021).
PubMed: 33712586

Assembly members:

Assembly members:
Receptor-interacting serine/threonine-protein kinase 3, polymer, 84 residues, 9454.359 Da.

Natural source:

Natural source: Common Name: Mouse Taxonomy ID: 10090 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Mus musculus

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: HHHHHHGPHPQRNQGDGRHG TPWYPWTPPNPMTGPPALVF NNCSEVQIGNYNSLVAPPRT TASSSAKYDQAQFGRGRGWQ PFHK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	90
15N chemical shifts	22

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, chain 1	1
2	entity_1, chain 2	1
3	entity_1, chain 3	1
4	entity_1, chain 4	1
5	entity_1, chain 5	1

Entities:

Entity 1, entity_1, chain 1 84 residues - 9454.359 Da.

1

HIS

GLY

PRO

HIS

PRO

2

GLN

ARG

ASN

GLN

GLY

ASP

GLY

ARG

HIS

GLY

3

THR

PRO

TRP

TYR

PRO

TRP

THR

PRO

ASN

4

PRO

MET

THR

GLY

PRO

ALA

LEU

VAL

PHE

5

ASN

CYS

SER

GLU

VAL

GLN

ILE

GLY

ASN

6

TYR

ASN

SER

LEU

VAL

ALA

PRO

ARG

THR

7

THR

ALA

SER

ALA

LYS

TYR

ASP

GLN

8

ALA

GLN

PHE

GLY

ARG

GLY

ARG

GLY

TRP

GLN

9

PRO

PHE

HIS

LYS

Samples:

sample_1: mouse rip3 fibril, [U-99% 13C; U-99% 15N], 0.95 – 1.05 mg/mL; H2O 100%

sample_2: mouse rip3 fibril, [99% 2-13C Glycerol, U-99% 15N], 0.95 – 1.05 mg/mL; H2O 100%

sample_3: mouse rip3 fibril, [99% 1,3-13C Glycerol; U-99% 15N], 0.95 – 1.05 mg/mL; H2O 100%

sample_4: mouse rip3 fibril, [U-50% 13C; natural abundance N][natural abundance C13, U-50% N15], 0.95 – 1.05 mg/mL; H2O 100%

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

Experiments:

Name	Sample	Sample state	Sample conditions
2D CC DARR	sample_1	anisotropic	sample_conditions_1
2D NCaCX	sample_1	anisotropic	sample_conditions_1
2D NCoCX	sample_1	anisotropic	sample_conditions_1
3D NCACX	sample_1	anisotropic	sample_conditions_1
3D NCOCX	sample_1	anisotropic	sample_conditions_1
2D CC DARR	sample_4	anisotropic	sample_conditions_1
2D NC TEDOR	sample_4	anisotropic	sample_conditions_1
2D NCoCX	sample_3	anisotropic	sample_conditions_1
2D NCaCX	sample_3	anisotropic	sample_conditions_1
2D CC DARR	sample_3	anisotropic	sample_conditions_1
2D NCoCX	sample_2	anisotropic	sample_conditions_1
2D NCaCX	sample_2	anisotropic	sample_conditions_1
2D CC DARR	sample_2	anisotropic	sample_conditions_1
2D NC TEDOR	sample_2	anisotropic	sample_conditions_1
2D NC TEDOR	sample_1	anisotropic	sample_conditions_1
2D NC TEDOR	sample_3	anisotropic	sample_conditions_1
2D ChhC	sample_4	anisotropic	sample_conditions_1
2D NCaCX	sample_1	anisotropic	sample_conditions_1
2D CC DARR	sample_1	anisotropic	sample_conditions_1
2D NCoCX	sample_1	anisotropic	sample_conditions_1
3D NCACX	sample_1	anisotropic	sample_conditions_1
3D NCOCX	sample_1	anisotropic	sample_conditions_1

Software:

Sparky, Goddard - peak picking

TopSpin, Bruker Biospin - collection

X-PLOR NIH v2.50, Schwieters, Kuszewski, Tjandra and Clore - refinement

xplor-nih v2.48, Schwieters, Kuszewski, Tjandra and Clore - structure calculation

NMR spectrometers:

Bruker Avance 700 MHz
Bruker Avance 700 MHz
Agilent DD2 700 MHz