8Z93 | pdb_00008z93

Cryo-EM structure of amyloid fibril formed by human RIPK1 RHIM protein

PDB DOI: https://doi.org/10.2210/pdb8Z93/pdb
EM Map EMD-39853: EMDB EMDataResource

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

Deposited: 2024-04-22 Released: 2025-04-30
Deposition Author(s): Ma, Y., Zhao, K., Liu, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.65 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM structure of amyloid fibril formed by human RIPK1 RHIM protein

Ma, Y., Zhao, K., Liu, C.

To be published.

Macromolecule Content

Total Structure Weight: 32.75 kDa
Atom Count: 477
Modeled Residue Count: 60
Deposited Residue Count: 294
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B, C	98	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13546
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.65 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-30

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	82188101

Revision History (Full details and data files)

Version 1.0: 2025-04-30
Type: Initial release
Version 1.1: 2025-07-16
Changes: Data collection

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.