9HR6 | pdb_00009hr6

cryoEM structure of amyloid fibrils formed by human RIPK1

PDB DOI: https://doi.org/10.2210/pdb9HR6/pdb
EM Map EMD-52356: EMDB EMDataResource

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

Deposited: 2024-12-17 Released: 2025-09-17
Deposition Author(s): Lopez-Alonso, J.P., Ubarretxena-Belandia, I., Jiang, H.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.57 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

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

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

Literature

Molecular Structure of Human Receptor Interacting Protein Kinase 1 (RIPK1) in its Fibrillar Conformation Elucidated by Solid-State NMR and Cryo-Electron Microscopy

Polonio, P., Lopez-Alonso, J.P., Ubarretxena-Belandia, I., Jiang, H., Escobedo-Gonzales, F.C., Titaux-Delgado, G.A., Mompean, M.

To be published.

Macromolecule Content

Total Structure Weight: 48.28 kDa
Atom Count: 930
Modeled Residue Count: 120
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

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(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, D, E	88	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: 2.57 Å
Aggregation State: HELICAL ARRAY
Reconstruction Method: HELICAL

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.6.2
MODEL REFINEMENT	Coot	0.9.2
MODEL REFINEMENT	PHENIX	1.21

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Lopez-Alonso, J.P.

Ubarretxena-Belandia, I.

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	--

Revision History (Full details and data files)

Version 1.0: 2025-09-17
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.