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- PDB-12dl: Native structure of the cytoplasmic lattice (CPL) asymmetric unit... -

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Basic information

Entry
Database: PDB / ID: 12dl
TitleNative structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
Components
  • (F-box and WD-40 domain protein ...) x 2
  • (NACHT, LRR and PYD domains-containing protein ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • Expressed sequence C85627
  • 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
KeywordsCYTOSOLIC PROTEIN / cytoplasmic lattice / egg / filamentous assembly
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 / The role of GTSE1 in G2/M progression after G2 checkpoint / embryonic cleavage / apical cortex / Recycling pathway of L1 / positive regulation of meiotic nuclear division / chromosomal DNA methylation maintenance following DNA replication / 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 / Hedgehog 'off' state / RHO GTPases Activate Formins / F-box domain binding / 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 ...: / 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. / : / A Receptor for Ubiquitination Targets / F-box domain profile. / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / F-box-like / NACHT nucleoside triphosphatase / F-box-like domain superfamily / 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 / F-box 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 / Tubulin/FtsZ family, GTPase domain / Ring finger / 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
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / F-box domain-containing protein / F-box domain-containing protein / Inactive protein-arginine deiminase type-6 ...GUANOSINE-5'-TRIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / F-box domain-containing protein / F-box domain-containing protein / 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 / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLi, Y. / Zheng, W. / Leem, J. / Wu, C. / Tang, S. / Mogessie, B. / Xiong, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Cytoplasmic lattices store developmentally poised degradative and cytoskeletal complexes in mammalian eggs.
Authors: Yujie Li / Wei Zheng / Jiyeon Leem / Chunxiang Wu / Shaogeng Tang / Binyam Mogessie / Yong Xiong /
Abstract: The cytoplasmic lattice (CPL) in mammalian eggs is essential for early embryonic development but its molecular components, structural organization and functional capacity have remained elusive. Here, ...The cytoplasmic lattice (CPL) in mammalian eggs is essential for early embryonic development but its molecular components, structural organization and functional capacity have remained elusive. Here, using cryo-electron microscopy, we show that the CPL filament in mouse metaphase II eggs contains repeating units with a periodicity of ~37 nm and determine its high-resolution, native structure and complete subunit composition. The CPL architecture organizes maternal-effect proteins, ubiquitination machinery and tubulin into a highly structured reservoir. Maternal-effect proteins form the scaffold of the CPL to sequester a UHRF1-UBE2D3 E3-E2 ubiquitination module and three distinct FBXW-SKP1 E3 ubiquitin ligase components, notably all in activity-excluded states. The CPL further contains αβ-tubulin heterodimers in a GTP-bound state, indicating microtubule-assembly-competent tubulin held in reserve. CPL filaments are capped by a terminal unit that lacks a PADI6 dimer, a scaffold component, suggesting a structural mechanism that prevents further oligomerization. Interactions between neighboring CPL filaments promote the assembly of a three-dimensional network in the egg cytoplasm. Taken together, our work defines how CPL assembly and architecture prime mammalian eggs for ubiquitin-mediated protein degradation and cytoskeletal remodeling during the egg-to-embryo transition.
History
DepositionMar 29, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
FA: Tubulin beta-4B chain
GB: NACHT, LRR and PYD domains-containing protein 5
GA: NACHT, LRR and PYD domains-containing protein 5
IA: Oocyte-expressed protein homolog
HB: Transducin-like enhancer protein 6
HA: Transducin-like enhancer protein 6
KA: Zinc finger BED domain-containing protein 3
LA: KH domain-containing protein 3
MA: NLR family, pyrin domain containing 4F
AC: Inactive protein-arginine deiminase type-6
AD: Inactive protein-arginine deiminase type-6
AE: Inactive protein-arginine deiminase type-6
AF: Inactive protein-arginine deiminase type-6
AG: Inactive protein-arginine deiminase type-6
AH: Inactive protein-arginine deiminase type-6
AA: Inactive protein-arginine deiminase type-6
AB: Inactive protein-arginine deiminase type-6
AI: Inactive protein-arginine deiminase type-6
AJ: Inactive protein-arginine deiminase type-6
EA: Tubulin alpha-1C chain
DA: NACHT, LRR and PYD domains-containing protein 14
DB: NACHT, LRR and PYD domains-containing protein 14
BA: E3 ubiquitin-protein ligase UHRF1
BB: E3 ubiquitin-protein ligase UHRF1
CA: Ubiquitin-conjugating enzyme E2 D3
CB: Ubiquitin-conjugating enzyme E2 D3
OA: F-box and WD-40 domain protein 19
QB: S-phase kinase-associated protein 1
QA: S-phase kinase-associated protein 1
NA: Expressed sequence C85627
QC: S-phase kinase-associated protein 1
PA: F-box and WD-40 domain protein 21
JA: Oocyte-expressed protein homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,137,88149
Polymers2,136,02733
Non-polymers1,85516
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 12 types, 27 molecules FAIAJAHBHAKALAMAACADAEAFAGAHAAABAIAJEABABBCACBQBQAQCNA

#1: 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
#3: 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
#4: 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
#5: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 25512.180 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#6: 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
#7: Protein NLR family, pyrin domain containing 4F


Mass: 108001.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#8: 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
#9: 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
#11: Protein E3 ubiquitin-protein ligase UHRF1 / Nuclear protein 95 / Nuclear zinc finger protein Np95 / Ubiquitin-like PHD and RING finger domain- ...Nuclear protein 95 / Nuclear zinc finger protein Np95 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase
#12: 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.: 2 / 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
#14: 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.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTX5
#15: Protein Expressed sequence C85627 / F-box and WD-40 domain protein 18


Mass: 54205.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3TSA9

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NACHT, LRR and PYD domains-containing protein ... , 2 types, 4 molecules GBGADADB

#2: 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
#10: 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.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6B966

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F-box and WD-40 domain protein ... , 2 types, 2 molecules OAPA

#13: Protein F-box and WD-40 domain protein 19


Mass: 53657.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8C2W8
#16: Protein F-box and WD-40 domain protein 21


Mass: 54517.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BI38

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Non-polymers , 4 types, 16 molecules

#17: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#18: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.4
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: 2500 nm / Nominal defocus min: 1800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 249541 / Symmetry type: POINT
RefinementHighest resolution: 3.5 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004136180
ELECTRON MICROSCOPYf_angle_d0.569184502
ELECTRON MICROSCOPYf_dihedral_angle_d5.25217934
ELECTRON MICROSCOPYf_chiral_restr0.04420758
ELECTRON MICROSCOPYf_plane_restr0.00423626

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