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- EMDB-67233: The focused structure of the C-terminal lobe of the human UBR4-KC... -

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Basic information

Entry
Database: EMDB / ID: EMD-67233
TitleThe focused structure of the C-terminal lobe of the human UBR4-KCMF1-Calmodulin complex
Map data
Sample
  • Complex: UBR4 complex with KCMF1 and calmodulin
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4
    • Protein or peptide: Calmodulin-1
  • Ligand: CALCIUM ION
KeywordsUbiquitinalytion / LIGASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsHu Z / Yan R
Funding support China, 1 items
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, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67233.png

Downloads & links

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Map

FileDownload / File: emd_67233.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 520 pix.
= 430.04 Å		0.83 Å/pix.
x 520 pix.
= 430.04 Å		0.83 Å/pix.
x 520 pix.
= 430.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.0888035 - 1.9320107
Average (Standard dev.)-0.0011599602 (±0.03374292)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 430.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67233_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67233_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : UBR4 complex with KCMF1 and calmodulin

EntireName: UBR4 complex with KCMF1 and calmodulin
Components
  • Complex: UBR4 complex with KCMF1 and calmodulin
    • Protein or peptide: E3 ubiquitin-protein ligase UBR4
    • Protein or peptide: Calmodulin-1
  • Ligand: CALCIUM ION

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Supramolecule #1: UBR4 complex with KCMF1 and calmodulin

SupramoleculeName: UBR4 complex with KCMF1 and calmodulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: E3 ubiquitin-protein ligase UBR4

MacromoleculeName: E3 ubiquitin-protein ligase UBR4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 173.301578 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GSKEKYRQLR DLHTLDSHVR GIKKLLEEQG IFLRASVVTA SSGSALQYDT LISLMEHLKA CAEIAAQRTI NWQKFCIKDD SVLYFLLQV SFLVDEGVSP VLLQLLSCAL CGSKVLAALA ASSGSSSASS SSAPVAASSG QATTQSKSST KKSKKEEKEK E KDGETSGS ...String:
GSKEKYRQLR DLHTLDSHVR GIKKLLEEQG IFLRASVVTA SSGSALQYDT LISLMEHLKA CAEIAAQRTI NWQKFCIKDD SVLYFLLQV SFLVDEGVSP VLLQLLSCAL CGSKVLAALA ASSGSSSASS SSAPVAASSG QATTQSKSST KKSKKEEKEK E KDGETSGS QEDQLCTALV NQLNKFADKE TLIQFLRCFL LESNSSSVRW QAHCLTLHIY RNSSKSQQEL LLDLMWSIWP EL PAYGRKA AQFVDLLGYF SLKTPQTEKK LKEYSQKAVE ILRTQNHILT NHPNSNIYNT LSGLVEFDGY YLESDPCLVC NNP EVPFCY IKLSSIKVDT RYTTTQQVVK LIGSHTISKV TVKIGDLKRT KMVRTINLYY NNRTVQAIVE LKNKPARWHK AKKV QLTPG QTEVKIDLPL PIVASNLMIE FADFYENYQA STETLQCPRC SASVPANPGV CGNCGENVYQ CHKCRSINYD EKDPF LCNA CGFCKYARFD FMLYAKPCCA VDPIENEEDR KKAVSNINTL LDKADRVYHQ LMGHRPQLEN LLCKVNEAAP EKPQDD SGT AGGISSTSAS VNRYILQLAQ EYCGDCKNSF DELSKIIQKV FASRKELLEY DLQQREAATK SSRTSVQPTF TASQYRA LS VLGCGHTSST KCYGCASAVT EHCITLLRAL ATNPALRHIL VSQGLIRELF DYNLRRGAAA MREEVRQLMC LLTRDNPE A TQQMNDLIIG KVSTALKGHW ANPDLASSLQ YEMLLLTDSI SKEDSCWELR LRCALSLFLM AVNIKTPVVV ENITLMCLR ILQKLIKPPA PTSKKNKDVP VEALTTVKPY CNEIHAQAQL WLKRDPKASY DAWKKCLPIR GIDGNGKAPS KSELRHLYLT EKYVWRWKQ FLSRRGKRTS PLDLKLGHNN WLRQVLFTPA TQAARQAACT IVEALATIPS RKQQVLDLLT SYLDELSIAG E CAAEYLAL YQKLITSAHW KVYLAARGVL PYVGNLITKE IARLLALEEA TLSTDLQQGY ALKSLTGLLS SFVEVESIKR HF KSRLVGT VLNGYLCLRK LVVQRTKLID ETQDMLLEML EDMTTGTESE TKAFMAVCIE TAKRYNLDDY RTPVFIFERL CSI IYPEEN EVTEFFVTLE KDPQQEDFLQ GRMPGNPYSS NEPGIGPLMR DIKNKICQDC DLVALLEDDS GMELLVNNKI ISLD LPVAE VYKKVWCTTN EGEPMRIVYR MRGLLGDATE EFIESLDSTT DEEEDEEEVY KMAGVMAQCG GLECMLNRLA GIRDF KQGR HLLTVLLKLF SYCVKVKVNR QQLVKLEMNT LNVMLGTLNL ALVAEQESKD SGGAAVAEQV LSIMEIILDE SNAEPL SED KGNLLLTGDK DQLVMLLDQI NSTFVRSNPS VLQGLLRIIP YLSFGEVEKM QILVERFKPY CNFDKYDEDH SGDDKVF LD CFCKIAAGIK NNSNGHQLKD LILQKGITQN ALDYMKKHIP SAKNLDADIW KKFLSRPALP FILRLLRGLA IQHPGTQV L IGTDSIPNLH KLEQVSSDEG I

UniProtKB: E3 ubiquitin-protein ligase UBR4

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Macromolecule #2: Calmodulin-1

MacromoleculeName: Calmodulin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.852545 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADQLTEEQI AEFKEAFSLF DKDGDGTITT KELGTVMRSL GQNPTEAELQ DMINEVDADG NGTIDFPEFL TMMARKMKDT DSEEEIREA FRVFDKDGNG YISAAELRHV MTNLGEKLTD EEVDEMIREA DIDGDGQVNY EEFVQMMTAK

UniProtKB: Calmodulin-1

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 244291
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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