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- PDB-9hxw: Cryo-EM structure of the human UBR4/KCMF1/CALM1 complex (composit... -

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Basic information

Entry
Database: PDB / ID: 9hxw
TitleCryo-EM structure of the human UBR4/KCMF1/CALM1 complex (composite map)
Components
  • Calmodulin-1
  • E3 ubiquitin-protein ligase KCMF1
  • E3 ubiquitin-protein ligase UBR4
KeywordsLIGASE / Ubiquitin ligase Protein quality control
Function / homology
Function and homology information


negative regulation of HRI-mediated signaling / synaptic signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination ...negative regulation of HRI-mediated signaling / synaptic signaling / ubiquitin-dependent protein catabolic process via the N-end rule pathway / protein K27-linked ubiquitination / cytoplasm protein quality control by the ubiquitin-proteasome system / protein branched polyubiquitination / negative regulation of fatty acid biosynthetic process / endosome organization / cytoplasm protein quality control / protein K11-linked ubiquitination / CaM pathway / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / Activation of Ca-permeable Kainate Receptor / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of high voltage-gated calcium channel activity / PKA activation / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / CLEC7A (Dectin-1) induces NFAT activation / Activation of RAC1 downstream of NMDARs / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / mitochondrion-endoplasmic reticulum membrane tethering / autophagosome membrane docking / negative regulation of calcium ion export across plasma membrane / regulation of cardiac muscle cell action potential / presynaptic endocytosis / Synthesis of IP3 and IP4 in the cytosol / regulation of cell communication by electrical coupling involved in cardiac conduction / Phase 0 - rapid depolarisation / calcineurin-mediated signaling / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / RHO GTPases activate PAKs / tertiary granule membrane / Ion transport by P-type ATPases / Uptake and function of anthrax toxins / regulation of ryanodine-sensitive calcium-release channel activity / Long-term potentiation / protein phosphatase activator activity / ficolin-1-rich granule membrane / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / protein K63-linked ubiquitination / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / catalytic complex / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein K48-linked ubiquitination / specific granule membrane / calcium channel inhibitor activity / Activation of AMPK downstream of NMDARs / cellular response to interferon-beta / presynaptic cytosol / Protein methylation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / eNOS activation / titin binding / Ion homeostasis / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / regulation of calcium-mediated signaling / sperm midpiece / voltage-gated potassium channel complex / positive regulation of autophagy / FCERI mediated Ca+2 mobilization / calcium channel complex / substantia nigra development / regulation of heart rate / Ras activation upon Ca2+ influx through NMDA receptor / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / adenylate cyclase activator activity / sarcomere / protein serine/threonine kinase activator activity / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / regulation of cytokinesis / spindle microtubule / positive regulation of receptor signaling pathway via JAK-STAT / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / RAF activation / Transcriptional activation of mitochondrial biogenesis / response to calcium ion / RING-type E3 ubiquitin transferase / cellular response to type II interferon / G2/M transition of mitotic cell cycle / Stimuli-sensing channels / long-term synaptic potentiation / spindle pole / ubiquitin-protein transferase activity
Similarity search - Function
E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 ...E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / Drought induced 19 protein type, zinc-binding domain / Drought induced 19 protein (Di19), zinc-binding / : / E3 ubiquitin-protein ligase UBR4-like domain / E3 ubiquitin ligase UBR4, C-terminal / E3 ubiquitin ligase UBR4-like / E3 ubiquitin-protein ligase UBR4 / UBR4 E3 catalytic module profile. / : / Putative zinc finger in N-recognin (UBR box) / Zinc finger, UBR-type / Zinc finger UBR-type profile. / Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway / Zinc finger ZZ-type signature. / Zinc finger, ZZ type / Zinc-binding domain, present in Dystrophin, CREB-binding protein. / Zinc finger, ZZ-type / Zinc finger, ZZ-type superfamily / Zinc finger ZZ-type profile. / zinc finger / : / Zinc finger C2H2 type domain profile. / Zinc finger C2H2-type / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Armadillo-type fold / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
Calmodulin-1 / E3 ubiquitin-protein ligase UBR4 / E3 ubiquitin-protein ligase KCMF1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGrabarczyk, D.B. / Clausen, T.
Funding support Austria, European Union, 2items
OrganizationGrant numberCountry
Austrian Research Promotion Agency852936 Austria
H2020 Marie Curie Actions of the European Commission847548European Union
CitationJournal: To Be Published
Title: Architecture of the UBR4 complex, a giant E4 ligase central to eukaryotic protein quality control
Authors: 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.
History
DepositionJan 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: E3 ubiquitin-protein ligase KCMF1
E: Calmodulin-1
F: Calmodulin-1
A: E3 ubiquitin-protein ligase UBR4
C: E3 ubiquitin-protein ligase KCMF1
B: E3 ubiquitin-protein ligase UBR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,168,11626
Polymers1,166,8086
Non-polymers1,30820
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein E3 ubiquitin-protein ligase KCMF1 / FGF-induced in gastric cancer / Potassium channel modulatory factor / PCMF / ZZ-type zinc finger- ...FGF-induced in gastric cancer / Potassium channel modulatory factor / PCMF / ZZ-type zinc finger-containing protein 1


Mass: 36674.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KCMF1, FIGC, ZZZ1 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9P0J7, RING-type E3 ubiquitin transferase
#2: Protein Calmodulin-1


Mass: 17980.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CALM1, CALM, CAM, CAM1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0DP23
#3: Protein E3 ubiquitin-protein ligase UBR4 / 600 kDa retinoblastoma protein-associated factor / p600 / N-recognin-4 / Retinoblastoma-associated ...600 kDa retinoblastoma protein-associated factor / p600 / N-recognin-4 / Retinoblastoma-associated factor of 600 kDa / RBAF600


Mass: 528748.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBR4, KIAA0462, KIAA1307, RBAF600 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q5T4S7, RING-type E3 ubiquitin transferase
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: UBR4/KCMF1/CALM1 ubiquitin ligase complex / Type: COMPLEX / Entity ID: #2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1638723 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00369836
ELECTRON MICROSCOPYf_angle_d0.69594552
ELECTRON MICROSCOPYf_dihedral_angle_d4.8669359
ELECTRON MICROSCOPYf_chiral_restr0.04211012
ELECTRON MICROSCOPYf_plane_restr0.00412076

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