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- PDB-9xtj: Overall structure of the human UBR4-KCMF1-Calmodulin complex -

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Basic information

Entry
Database: PDB / ID: 9xtj
TitleOverall structure of the human UBR4-KCMF1-Calmodulin complex
Components
  • Calmodulin-1
  • E3 ubiquitin-protein ligase KCMF1
  • E3 ubiquitin-protein ligase UBR4
KeywordsLIGASE / Ubiquitinalytion
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 / HRI-mediated signaling / 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 / HRI-mediated signaling / 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 / protein K27-linked ubiquitination / 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 / PKA activation / CaMK IV-mediated phosphorylation of CREB / CASP4 inflammasome assembly / Glycogen breakdown (glycogenolysis) / negative regulation of ryanodine-sensitive calcium-release channel activity / Activation of RAC1 downstream of NMDARs / organelle localization by membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / : / negative regulation of high voltage-gated calcium channel activity / 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 / Phase 0 - rapid depolarisation / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / calcineurin-mediated signaling / RHO GTPases activate PAKs / protein quality control for misfolded or incompletely synthesized proteins / regulation of cell communication by electrical coupling involved in cardiac conduction / tertiary granule membrane / Uptake and function of anthrax toxins / Ion transport by P-type ATPases / protein phosphatase activator activity / Long-term potentiation / ficolin-1-rich granule membrane / Calcineurin activates NFAT / regulation of ryanodine-sensitive calcium-release channel activity / DARPP-32 events / Regulation of MECP2 expression and activity / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta / specific granule membrane / protein K63-linked ubiquitination / Dengue virus activates/modulates innate and adaptive immune responses / presynaptic cytosol / RHO GTPases activate IQGAPs / catalytic complex / calcium channel inhibitor activity / ubiquitin-like ligase-substrate adaptor activity / eNOS activation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / Activation of AMPK downstream of NMDARs / Ion homeostasis / regulation of heart rate / Protein methylation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / titin binding / protein K48-linked ubiquitination / calcium channel complex / voltage-gated potassium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / positive regulation of autophagy / FCGR3A-mediated IL10 synthesis / protein serine/threonine kinase activator activity / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / positive regulation of receptor signaling pathway via JAK-STAT / calyx of Held / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / regulation of cytokinesis / VEGFR2 mediated cell proliferation / spindle microtubule / VEGFR2 mediated vascular permeability / sarcomere / calcium channel regulator activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / myelin sheath / cellular response to type II interferon / Transcriptional activation of mitochondrial biogenesis / long-term synaptic potentiation / Enterobacterial factors antagonize host defense / RAF activation
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: 3.89 Å
AuthorsHu, Z. / Yan, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Protein Cell / Year: 2026
Title: Structural and mechanistic insights into the UBR4-KCMF1-Calmodulin complex.
Authors: Ziwei Hu / Zhiheng Liu / Jiali Xu / Baotong Zhang / Renhong Yan /
History
DepositionNov 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,271,05510
Polymers1,270,8956
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: 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: 576602.375 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: Homo sapiens (human)
References: UniProt: Q5T4S7, RING-type E3 ubiquitin transferase
#2: 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: 41992.348 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: Homo sapiens (human)
References: UniProt: Q9P0J7, RING-type E3 ubiquitin transferase
#3: Protein Calmodulin-1


Mass: 16852.545 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: Homo sapiens (human) / References: UniProt: P0DP23
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
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: Human UBR4-KCMF1-Calmodulin complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244291 / Symmetry type: POINT
RefinementHighest resolution: 3.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00572208
ELECTRON MICROSCOPYf_angle_d0.72697778
ELECTRON MICROSCOPYf_dihedral_angle_d4.1849668
ELECTRON MICROSCOPYf_chiral_restr0.04211334
ELECTRON MICROSCOPYf_plane_restr0.00412549

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