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

Validation slider image for 8Z93

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

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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% 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: 4.65 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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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

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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.