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- PDB-9t65: Complex linking two cytoplasmic lattice filaments -

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Basic information

Entry
Database: PDB / ID: 9t65
TitleComplex linking two cytoplasmic lattice filaments
Components
  • E3 ubiquitin-protein ligase UHRF1
  • F-box/WD repeat-containing protein
  • Inactive protein-arginine deiminase type-6
  • NACHT, LRR and PYD domains-containing protein 14
  • S-phase kinase-associated protein 1
KeywordsUNKNOWN FUNCTION / Ubiquitination / Complex / Filament
Function / homology
Function and homology information


regulation of translation by machinery localization / cytoplasm organization / ooplasm / Prolactin receptor signaling / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of BACH1 activity ...regulation of translation by machinery localization / cytoplasm organization / ooplasm / Prolactin receptor signaling / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of BACH1 activity / histone H3K18 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3K23 ubiquitin ligase activity / SCF(Skp2)-mediated degradation of p27/p21 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / histone H3 reader activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / cortical granule / Orc1 removal from chromatin / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / Iron uptake and transport / embryonic cleavage / chromosomal DNA methylation maintenance following DNA replication / intermediate filament cytoskeleton / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / F-box domain binding / Downstream TCR signaling / hemi-methylated DNA-binding / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / regulation of epithelial cell proliferation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Neddylation / PcG protein complex / gap junction / maintenance of protein location in nucleus / positive regulation of epithelial cell apoptotic process / Cul7-RING ubiquitin ligase complex / methyl-CpG binding / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin ligase activator activity / epigenetic programming in the zygotic pronuclei / histone H3K9me2/3 reader activity / negative regulation of gene expression via chromosomal CpG island methylation / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / positive regulation of protein metabolic process / ubiquitin ligase complex scaffold activity / mitotic spindle assembly / protein monoubiquitination / cullin family protein binding / cis-regulatory region sequence-specific DNA binding / protein autoubiquitination / ubiquitin-like ligase-substrate adaptor activity / cytoskeleton organization / protein localization to chromatin / heterochromatin / protein K48-linked ubiquitination / in utero embryonic development / replication fork / molecular function activator activity / euchromatin / tubulin binding / RING-type E3 ubiquitin transferase / beta-catenin binding / intracellular protein localization / nuclear matrix / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / regulation of inflammatory response / heterochromatin formation / spermatogenesis / ubiquitin-dependent protein catabolic process / histone binding / nucleic acid binding / proteasome-mediated ubiquitin-dependent protein catabolic process / cell differentiation / protein ubiquitination / chromatin remodeling / protein domain specific binding / DNA repair / apoptotic process / centrosome / calcium ion binding / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA-templated transcription
Similarity search - Function
: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily ...: / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / PUA-like superfamily / PHD-finger / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger PHD-type signature. / SKP1/BTB/POZ domain superfamily / Ring finger / Cupredoxin / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Leucine-rich repeat / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Leucine-rich repeat domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NACHT, LRR and PYD domains-containing protein 14 / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / S-phase kinase-associated protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 5.6 Å
AuthorsSingh, K. / Harasimov, K. / Carter, A.P.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 426-2023European Union
Wellcome Trust221856/Z/20/Z United Kingdom
CitationJournal: EMBO J / Year: 2026
Title: In-situ cryo-ET of mouse embryos reveals cytoplasmic lattices contain ubiquitin-charged E2-E3 ligase assemblies.
Authors: Kashish Singh / Katarina Harasimov / Kathy K Niakan / Andrew P Carter /
Abstract: Cytoplasmic lattices (CPLs) are filamentous assemblies essential for mammalian embryonic development. They are known to regulate organelle organization, spindle assembly, and protein homeostasis, but ...Cytoplasmic lattices (CPLs) are filamentous assemblies essential for mammalian embryonic development. They are known to regulate organelle organization, spindle assembly, and protein homeostasis, but their molecular functions remain unclear. Here, we develop a strategy combining cryo-focused ion beam milling and cryo-electron tomography to resolve macromolecular complexes directly in mammalian embryos. Using this approach, we determine the in situ structure of cytoplasmic lattices within 6/8-cell mouse embryos at ~4.7 Å resolution. CPL filaments are built from multiple copies of at least fourteen proteins arranged into a ~4.5 MDa repeating unit. The repeat contains a central cavity that is open at the back and lined with multiple FBXW-SKP1 complexes and three modules, each containing the E2 ubiquitin-conjugating enzyme UBE2D and the E3 ligase UHRF1. We resolve two CPL states: one is consistent with a ubiquitin-charged UBE2D, where ubiquitin is held in an open, inactive conformation by binding the scaffold protein PADI6; the second lacks discernible ubiquitin density and shows structural changes compatible with ubiquitin becoming available for transfer. Our findings support a model in which CPLs function as large ubiquitin ligase assemblies during early embryonic development.
History
DepositionNov 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inactive protein-arginine deiminase type-6
B: Inactive protein-arginine deiminase type-6
C: Inactive protein-arginine deiminase type-6
D: Inactive protein-arginine deiminase type-6
E: Inactive protein-arginine deiminase type-6
F: Inactive protein-arginine deiminase type-6
G: Inactive protein-arginine deiminase type-6
H: Inactive protein-arginine deiminase type-6
l: S-phase kinase-associated protein 1
n: NACHT, LRR and PYD domains-containing protein 14
o: E3 ubiquitin-protein ligase UHRF1
k: F-box/WD repeat-containing protein


Theoretical massNumber of molelcules
Total (without water)875,16812
Polymers875,16812
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Inactive protein-arginine deiminase type-6 / Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine ...Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine deiminase VI / Protein-arginine deiminase type VI / Protein-arginine deiminase type-6


Mass: 76854.109 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K3V4
#2: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / S-phase kinase-associated protein 1A / p19A / p19skp1


Mass: 18693.992 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTX5
#3: Protein NACHT, LRR and PYD domains-containing protein 14 / NALP-iota / Germ cell specific leucine-rich repeat NTPase


Mass: 113527.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6B966
#4: Protein E3 ubiquitin-protein ligase UHRF1 / Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / ...Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / mUhrf1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 88436.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase
#5: Protein F-box/WD repeat-containing protein


Mass: 39676.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Multi-subunit complex containing PADI6, SKP1, a F-box/WD repeat-containing protein, NLRP14 and UHRF1
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
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: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 3.5 e/Å2 / Avg electron dose per subtomogram: 115 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5.1volume selection
13RELION5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 5.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 86696 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 1153 / Num. of volumes extracted: 268774

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