Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control.
Journal, issue, pages	Science, Vol. 389, Issue 6763, Page 909-914, Year 2025
Publish date	Aug 28, 2025
Authors	Daniel B Grabarczyk / Julian F Ehrmann / Paul Murphy / Woo Seok Yang / Robert Kurzbauer / Lillie E Bell / Luiza Deszcz / Jana Neuhold / Alexander Schleiffer / Alexandra Shulkina / Juyeon Lee / Jin Seok Shin / Anton Meinhart / Gijs A Versteeg / Eszter Zavodszky / Hyun Kyu Song / Ramanujan S Hegde / Tim Clausen /
PubMed Abstract	Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome ...Eukaryotic cells have evolved sophisticated quality control mechanisms to eliminate aggregation-prone proteins that compromise cellular health. Central to this defense is the ubiquitin-proteasome system, where UBR4 acts as an essential E4 ubiquitin ligase, amplifying degradation marks on defective proteins. Cryo-electron microscopy analysis of UBR4 in complex with its cofactors KCMF1 and CALM1 reveals a massive 1.3-megadalton ring structure, featuring a central substrate-binding arena and flexibly attached catalytic units. Our structure shows how UBR4 binds substrate and extends lysine-48-specific ubiquitin chains. Efficient substrate targeting depends on both preubiquitination and specific N-degrons, with KCMF1 acting as a key substrate filter. The architecture of the E4 megacomplex is conserved across eukaryotes, but species-specific adaptations allow UBR4 to perform its precisely tuned quality control function in diverse cellular environments.
External links	Science / PubMed:40875847 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.5 - 7.7 Å
Structure data	EMDB-52488: Cryo-EM map of human UBR4/KCMF1/CALM1 in complex with UBE2A Method: EM (single particle) / Resolution: 5.9 Å EMDB-52491: Cryo-EM structure of UBR4/KCMF1/CALM1 (consensus map) Method: EM (single particle) / Resolution: 4.7 Å EMDB-52494: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (UBR/BS1/ZZ-DZB focused refinement) Method: EM (single particle) / Resolution: 5.6 Å EMDB-52504: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (consensus map) Method: EM (single particle) / Resolution: 4.2 Å EMDB-52513: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (BS1/UBR/ZZ-DZB focused refinement) Method: EM (single particle) / Resolution: 4.1 Å EMDB-52516: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term focused refinement) Method: EM (single particle) / Resolution: 3.0 Å 53348 9qt9 EMDB-53348, PDB-9qt9: Cryo-EM structure of the core of the Arabidopsis thaliana UBR4/DI19/CALM1 complex Method: EM (single particle) / Resolution: 3.9 Å EMDB-53425: Cryo-EM structure of the human UBR4 complex (ZZ-DZB deletion variant) Method: EM (single particle) / Resolution: 7.7 Å 53426 9qws EMDB-53426, PDB-9qws: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term dimer interface focused refinement) Method: EM (single particle) / Resolution: 3.1 Å 53428 9qwu EMDB-53428, PDB-9qwu: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (CALM1 focused refinement) Method: EM (single particle) / Resolution: 3.1 Å 53430 9qwx EMDB-53430, PDB-9qwx: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (N-term focused refinement) Method: EM (single particle) / Resolution: 3.6 Å 53431 9qwz EMDB-53431, PDB-9qwz: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (BP focused refinement) Method: EM (single particle) / Resolution: 4.8 Å 53432 9qx0 EMDB-53432, PDB-9qx0: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (C-term focused refinement) Method: EM (single particle) / Resolution: 3.4 Å 53433 9qx1 EMDB-53433, PDB-9qx1: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (C-term dimer interface focused refinement) Method: EM (single particle) / Resolution: 2.6 Å 53434 9qx2 EMDB-53434, PDB-9qx2: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (N-term focused refinement) Method: EM (single particle) / Resolution: 5.7 Å 53435 9qx5 EMDB-53435, PDB-9qx5: Cryo-EM structure of the C. elegans UBR4/KCMF1 complex (side focused refinement) Method: EM (single particle) / Resolution: 3.5 Å PDB-9jni: KCMF1 Zn-coordinating domains with RCKG peptide (Sulfonic Cysteine) Method: X-RAY DIFFRACTION / Resolution: 1.92 Å PDB-9lgs: R-degron fused ZZ-domain of the Arabidopsis thaliana E3 ubiquitin-protein ligase BIG Method: X-RAY DIFFRACTION / Resolution: 1.5 Å PDB-9upz: KCMF1 Zn-coordinating domains with RTGG peptide Method: X-RAY DIFFRACTION / Resolution: 1.71 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-HOH: WATER ChemComp-NI: NICKEL (II) ION
Source	homo sapiens (human) caenorhabditis elegans (invertebrata) arabidopsis thaliana (thale cress) synthetic construct (others)
Keywords	PEPTIDE BINDING PROTEIN / Complex / ZZ-domain / C2H2 Zn-finger domain / KCMF1 / Arg/N-degon pathway / LIGASE / Arabidopsis thaliana / BIG / E3-ubiquitin ligase / Ubiquitin ligase / Protein quality control / Arg/N-degron pathway