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- PDB-9t63: Asymmetric unit of a cytoplasmic lattice filament repeat unit -

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Entry
Database: PDB / ID: 9t63
TitleAsymmetric unit of a cytoplasmic lattice filament repeat unit
Components
  • (NACHT, LRR and PYD domains-containing protein ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • F-box/WD repeat-containing protein
  • Inactive protein-arginine deiminase type-6
  • KH domain-containing protein 3
  • NLR family, pyrin domain containing 4F
  • Oocyte-expressed protein homolog
  • S-phase kinase-associated protein 1
  • Transducin-like enhancer protein 6
  • Tubulin alpha-1C chain
  • Tubulin beta-4B chain
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsUNKNOWN FUNCTION / Ubiquitination / Complex / Filament
Function / homology
Function and homology information


regulation of translation by machinery localization / cytoplasm organization / ooplasm / Signaling by BMP / Prolactin receptor signaling / embryonic process involved in female pregnancy / subcortical maternal complex / establishment of organelle localization / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cargo trafficking to the periciliary membrane ...regulation of translation by machinery localization / cytoplasm organization / ooplasm / Signaling by BMP / Prolactin receptor signaling / embryonic process involved in female pregnancy / subcortical maternal complex / establishment of organelle localization / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cargo trafficking to the periciliary membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / establishment or maintenance of apical/basal cell polarity / endoplasmic reticulum localization / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / SCF-beta-TrCP mediated degradation of Emi1 / E3 ubiquitin ligases ubiquitinate target proteins / Downregulation of SMAD2/3:SMAD4 transcriptional activity / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of BACH1 activity / histone H3K18 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / histone H3K23 ubiquitin ligase activity / SCF(Skp2)-mediated degradation of p27/p21 / COPI-mediated anterograde transport / spermatogonial cell division / Regulation of TNFR1 signaling / MAP3K8 (TPL2)-dependent MAPK1/3 activation / histone H3 reader activity / Regulation of RUNX2 expression and activity / Kinesins / Degradation of GLI1 by the proteasome / IKK complex recruitment mediated by RIP1 / 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 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / PKR-mediated signaling / Aggrephagy / fertilization / regulation of establishment of protein localization / RHO GTPases activate IQGAPs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Degradation of beta-catenin by the destruction complex / COPI-dependent Golgi-to-ER retrograde traffic / Resolution of Sister Chromatid Cohesion / Activation of NF-kappaB in B cells / Iron uptake and transport / embryonic cleavage / The role of GTSE1 in G2/M progression after G2 checkpoint / apical cortex / positive regulation of meiotic nuclear division / chromosomal DNA methylation maintenance following DNA replication / Recycling pathway of L1 / positive regulation of embryonic development / regulation of RNA stability / intermediate filament cytoskeleton / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / axonemal microtubule / F-box domain binding / Hedgehog 'off' state / RHO GTPases Activate Formins / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Downstream TCR signaling / Separation of Sister Chromatids / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / AURKA Activation by TPX2 / Peroxisomal protein import / hemi-methylated DNA-binding / GLI3 is processed to GLI3R by the proteasome / embryonic pattern specification / Regulation of PLK1 Activity at G2/M Transition / regulation of epithelial cell proliferation / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Neddylation / PcG protein complex / MHC class II antigen presentation / gap junction / establishment of spindle localization
Similarity search - Function
Zinc finger BED domain-containing protein 2/3 / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like ...Zinc finger BED domain-containing protein 2/3 / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / 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. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / 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 / K Homology domain, type 1 superfamily / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / PUA-like superfamily / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / PHD-finger / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Death-like domain superfamily / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain superfamily / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Ring finger / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Cupredoxin / Tubulin/FtsZ, GTPase domain superfamily / 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 / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat
Similarity search - Domain/homology
NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / NACHT, LRR and PYD domains-containing protein 14 / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / KH domain-containing protein 3 / Zinc finger BED domain-containing protein 3 ...NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / NACHT, LRR and PYD domains-containing protein 14 / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / KH domain-containing protein 3 / Zinc finger BED domain-containing protein 3 / NACHT, LRR and PYD domains-containing protein 5 / S-phase kinase-associated protein 1 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.7 Å
AuthorsSingh, K. / Harasimov, K. / Carter, A.
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

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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
I: Inactive protein-arginine deiminase type-6
J: Inactive protein-arginine deiminase type-6
O: Oocyte-expressed protein homolog
R: Oocyte-expressed protein homolog
S: KH domain-containing protein 3
Y: NLR family, pyrin domain containing 4F
Z: NACHT, LRR and PYD domains-containing protein 14
b: Ubiquitin-conjugating enzyme E2 D3
f: S-phase kinase-associated protein 1
h: S-phase kinase-associated protein 1
T: Zinc finger BED domain-containing protein 3
a: E3 ubiquitin-protein ligase UHRF1
X: NLR family, pyrin domain containing 4F
M: NACHT, LRR and PYD domains-containing protein 5
N: Transducin-like enhancer protein 6
P: NACHT, LRR and PYD domains-containing protein 5
Q: Transducin-like enhancer protein 6
c: Tubulin alpha-1C chain
d: Tubulin beta-4B chain
g: F-box/WD repeat-containing protein
e: F-box/WD repeat-containing protein


Theoretical massNumber of molelcules
Total (without water)1,923,76929
Polymers1,923,76929
Non-polymers00
Water00
1


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

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Components

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Protein , 12 types, 26 molecules ABCDEFGHIJORSYXbfhTaNQcdge

#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.: 10 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K3V4
#2: Protein Oocyte-expressed protein homolog / Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific ...Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific protein 19 / mOEP19 / STAT3 downstream gene and differentiation regulator


Mass: 18481.295 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWE6
#3: Protein KH domain-containing protein 3 / Protein Filia


Mass: 48055.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWU5
#4: Protein NLR family, pyrin domain containing 4F


Mass: 108001.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#6: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16706.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P61079, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#7: 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.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTX5
#8: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 25643.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#9: 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
#11: Protein Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 65187.332 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WVB3
#12: Protein Tubulin alpha-1C chain / Alpha-tubulin 6 / Alpha-tubulin isotype M-alpha-6 / Tubulin alpha-6 chain


Mass: 49962.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68373, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#13: Protein Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372
#14: Protein F-box/WD repeat-containing protein


Mass: 39676.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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NACHT, LRR and PYD domains-containing protein ... , 2 types, 3 molecules ZMP

#5: 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
#10: Protein NACHT, LRR and PYD domains-containing protein 5 / Maternal antigen that embryos require / Mater protein / Ooplasm-specific protein 1 / OP1


Mass: 131468.547 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1M5

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Details

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: Asymmetric unit of the cytoplasmic lattice repeating unit
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: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 268774 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 1153 / Num. of volumes extracted: 268774

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