9HYF | pdb_00009hyf

Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (composite map)

PDB DOI: https://doi.org/10.2210/pdb9HYF/pdb
EM Map EMD-52502: EMDB EMDataResource

Classification: LIGASE
Organism(s): Caenorhabditis elegans
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-01-09 Released: 2026-05-27
Deposition Author(s): Grabarczyk, D.B., Clausen, T.
Funding Organization(s): Austrian Research Promotion Agency, H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9HYF

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

Literature

Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control

Grabarczyk, D.B., Ehrmann, J.F., Murphy, P., Kurzbauer, R., Bell, L.E., Deszcz, L., Neuhold, J., Schleiffer, A., Shulkina, A., Versteeg, G.A., Meinhart, A., Zavodszky, E., Hegde, R.S., Clausen, T.

To be published.

Macromolecule Content

Total Structure Weight: 1,000.87 kDa
Atom Count: 64,398
Modeled Residue Count: 8,016
Deposited Residue Count: 8,752
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBR-type domain-containing protein	A, C [auth B]	3,861	Caenorhabditis elegans	Mutation(s): 0 Gene Names: ubr-4, C44E4.1, CELE_C44E4.1
UniProt
Find proteins for A0A0S4XR36 (Caenorhabditis elegans) Explore A0A0S4XR36 Go to UniProtKB: A0A0S4XR36
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S4XR36
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase kcmf-1	B [auth C], D	515	Caenorhabditis elegans	Mutation(s): 0 Gene Names: kcmf-1, ZK652.6 EC: 2.3.2.27
UniProt
Find proteins for P34664 (Caenorhabditis elegans) Explore P34664 Go to UniProtKB: P34664
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34664
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain I [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain I [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain I [auth A]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth C], K [auth C], L [auth C], M [auth C], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth D], T [auth D], U [auth D], V [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

Deposition Author(s):

Grabarczyk, D.B.

Funding Organization	Location	Grant Number
Austrian Research Promotion Agency	Austria	852936
H2020 Marie Curie Actions of the European Commission	European Union	847548

Revision History (Full details and data files)

Version 1.0: 2026-05-27
Type: Initial release

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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.