9V9C | pdb_00009v9c

Cryo-EM structure of human TNFR1 DD filament

PDB DOI: https://doi.org/10.2210/pdb9V9C/pdb
EM Map EMD-64869: EMDB EMDataResource

Classification: PROTEIN FIBRIL
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-05-30 Released: 2026-04-08
Deposition Author(s): Zhao, K., Liu, J.P., Liu, C., Yuan, J.Y.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.62 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

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

Literature

Electric dipole moment drives the dynamics of the TNFR1 complex I signalosome

Zhao, K., Liu, J.P., Liu, C., Yuan, J.Y.

(2026) Nature

DOI: https://doi.org/10.1038/s41586-026-10304-1

Macromolecule Content

Total Structure Weight: 260.72 kDa
Atom Count: 14,360
Modeled Residue Count: 1,740
Deposited Residue Count: 2,280
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 1A, membrane form	A B C D E A, B, C, D, E, F, G [auth I], H [auth L], I [auth O], J [auth R], K [auth G], L [auth J], M, N [auth P], O [auth S], P [auth H], Q [auth K], R [auth N], S [auth Q], T	114	Homo sapiens	Mutation(s): 0 Gene Names: TNFRSF1A, TNFAR, TNFR1
UniProt & NIH Common Fund Data Resources
Find proteins for P19438 (Homo sapiens) Explore P19438 Go to UniProtKB: P19438
PHAROS: P19438 GTEx: ENSG00000067182
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P19438
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.62 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.15.2_3472

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-04-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-04-08
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.