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- PDB-9xti: The focused structure of the C-terminal lobe of the human UBR4-KC... -

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Basic information

Entry
Database: PDB / ID: 9xti
TitleThe focused structure of the C-terminal lobe of the human UBR4-KCMF1-Calmodulin complex
Components
  • Calmodulin-1
  • E3 ubiquitin-protein ligase UBR4
KeywordsLIGASE / Ubiquitinalytion
Function / homology
Function and homology information


negative regulation of HRI-mediated 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 ...negative regulation of HRI-mediated 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 / Sodium/Calcium exchangers / protein K27-linked ubiquitination / 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 / catalytic complex / Regulation of MECP2 expression and activity / DARPP-32 events / Smooth Muscle Contraction / detection of calcium ion / regulation of cardiac muscle contraction / cellular response to interferon-beta / specific granule membrane / RHO GTPases activate IQGAPs / Dengue virus activates/modulates innate and adaptive immune responses / calcium channel inhibitor activity / ubiquitin-like ligase-substrate adaptor activity / presynaptic cytosol / 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 / titin binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein K48-linked ubiquitination / voltage-gated potassium channel complex / calcium channel complex / FCERI mediated Ca+2 mobilization / substantia nigra development / FCGR3A-mediated IL10 synthesis / positive regulation of autophagy / protein serine/threonine kinase activator activity / sperm midpiece / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / calyx of Held / positive regulation of receptor signaling pathway via JAK-STAT / Ras activation upon Ca2+ influx through NMDA receptor / adenylate cyclase activator activity / regulation of cytokinesis / VEGFR2 mediated cell proliferation / VEGFR2 mediated vascular permeability / spindle microtubule / sarcomere / Translocation of SLC2A4 (GLUT4) to the plasma membrane / calcium channel regulator activity / myelin sheath / cellular response to type II interferon / Transcriptional activation of mitochondrial biogenesis / long-term synaptic potentiation / Enterobacterial factors antagonize host defense / response to calcium ion / RAF activation / RING-type E3 ubiquitin transferase
Similarity search - Function
E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / 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) ...E3 ubiquitin-protein ligase UBR4, N-terminal / : / E3 ubiquitin-protein ligase UBR4 N-terminal / : / 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 / : / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 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 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)380,4698
Polymers380,3084
Non-polymers1604
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
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: 173301.578 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 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
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationN

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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 complex with KCMF1 and calmodulin / Type: COMPLEX / Entity ID: #1-#2 / 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: NITROGEN

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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: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 244291 / Symmetry type: POINT
RefinementHighest resolution: 3.73 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00327056
ELECTRON MICROSCOPYf_angle_d0.58536568
ELECTRON MICROSCOPYf_dihedral_angle_d6.0043644
ELECTRON MICROSCOPYf_chiral_restr0.0394200
ELECTRON MICROSCOPYf_plane_restr0.0044708

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