9XON | pdb_00009xon

RIPK1 death domain filamentation drives TNF-induced apoptosis

PDB DOI: https://doi.org/10.2210/pdb9XON/pdb
EM Map EMD-67084: EMDB EMDataResource

Classification: APOPTOSIS
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-11-14 Released: 2026-10-14
Deposition Author(s): Liu, P., Tan, Y.B., Luo, D.
Funding Organization(s): National Research Foundation (NRF, Singapore)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9XON

This is version 1.0 of the entry. See complete history.

Literature

RIPK1 Death Domain Filamentation Drives TNF-Induced Apoptosis

Chen, Y., Liu, P., Tan, Y.B., Luo, D., Tergaonkar, V.

To be published.

Macromolecule Content

Total Structure Weight: 321.09 kDa
Atom Count: 20,600
Modeled Residue Count: 2,525
Deposited Residue Count: 2,775
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y	111	Homo sapiens	Mutation(s): 0 Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens) Explore Q13546 Go to UniProtKB: Q13546
PHAROS: Q13546 GTEx: ENSG00000137275
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13546
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.50 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487
MODEL REFINEMENT	Coot

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-14

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	NRF-CRP26-2021-0001

Revision History (Full details and data files)

Version 1.0: 2026-10-14
Type: Initial release