9HXW | pdb_00009hxw

Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (composite map)

PDB DOI: https://doi.org/10.2210/pdb9HXW/pdb
EM Map EMD-52490: EMDB EMDataResource

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2025-01-08 Released: 2025-12-10
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: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9HXW

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: 1,168.12 kDa
Atom Count: 68,636
Modeled Residue Count: 8,750
Deposited Residue Count: 10,540
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase KCMF1	A [auth D], E [auth C]	331	Homo sapiens	Mutation(s): 0 Gene Names: KCMF1, FIGC, ZZZ1 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P0J7 (Homo sapiens) Explore Q9P0J7 Go to UniProtKB: Q9P0J7
PHAROS: Q9P0J7 GTEx: ENSG00000176407
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9P0J7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	B [auth E], C [auth F]	158	Homo sapiens	Mutation(s): 0 Gene Names: CALM1, CALM, CAM, CAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23 Go to UniProtKB: P0DP23
PHAROS: P0DP23 GTEx: ENSG00000198668
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DP23
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UBR4	D [auth A], F [auth B]	4,781	Homo sapiens	Mutation(s): 0 Gene Names: UBR4, KIAA0462, KIAA1307, RBAF600 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q5T4S7 (Homo sapiens) Explore Q5T4S7 Go to UniProtKB: Q5T4S7
PHAROS: Q5T4S7 GTEx: ENSG00000127481
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5T4S7
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 Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain H [auth D] SDF format, chain G [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain H [auth D] MOL2 format, chain G [auth D] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain H [auth D] mmCIF format, chain G [auth D]	G [auth D] H [auth D] I [auth D] J [auth D] K [auth A] G [auth D], H [auth D], I [auth D], J [auth D], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-10

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: 2025-12-10
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.