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- PDB-9w2m: Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte -

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Basic information

Entry
Database: PDB / ID: 9w2m
TitleCryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte
Components
  • (Tubulin beta- ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • FBXW24
  • Inactive protein-arginine deiminase type-6
  • Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
  • KH domain-containing protein 3
  • NACHT, LRR and PYD domains-containing protein 14
  • NLR family, pyrin domain containing 4F
  • Oocyte-expressed protein homolog
  • S-phase kinase-associated protein 1
  • Transducin-like enhancer protein 6
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsSTRUCTURAL PROTEIN / Cytoplasmic lattice / Maternal complex / Cryo-EM structure / Protein assembly
Function / homology
Function and homology information


regulation of translation by machinery localization / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / establishment of organelle localization / Chromatin modifying enzymes / protein storage ...regulation of translation by machinery localization / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / establishment of organelle localization / Chromatin modifying enzymes / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / cortical granule exocytosis / embryonic process involved in female pregnancy / endoplasmic reticulum localization / ooplasm / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / establishment or maintenance of apical/basal cell polarity / SCF-beta-TrCP mediated degradation of Emi1 / COPI-independent Golgi-to-ER retrograde traffic / E3 ubiquitin ligases ubiquitinate target proteins / Downregulation of SMAD2/3:SMAD4 transcriptional activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cytoplasm organization / Regulation of BACH1 activity / histone H3K18 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / SCF(Skp2)-mediated degradation of p27/p21 / histone H3K23 ubiquitin ligase activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / COPI-mediated anterograde transport / spermatogonial cell division / Regulation of TNFR1 signaling / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Kinesins / histone H3 reader activity / Regulation of RUNX2 expression and activity / cortical granule / Degradation of GLI1 by the proteasome / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Orc1 removal from chromatin / IKK complex recruitment mediated by RIP1 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / PKR-mediated signaling / Aggrephagy / RHO GTPases activate IQGAPs / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / Recycling pathway of L1 / Iron uptake and transport / The role of GTSE1 in G2/M progression after G2 checkpoint / COPI-dependent Golgi-to-ER retrograde traffic / apical cortex / positive regulation of meiotic nuclear division / regulation of RNA stability / positive regulation of embryonic development / chromosomal DNA methylation maintenance following DNA replication / FCERI mediated NF-kB activation / CLEC7A (Dectin-1) signaling / Interleukin-1 signaling / Hedgehog 'off' state / RHO GTPases Activate Formins / F-box domain binding / Separation of Sister Chromatids / Downstream TCR signaling / Recruitment of NuMA to mitotic centrosomes / hemi-methylated DNA-binding / regulation of establishment of protein localization / Peroxisomal protein import / GLI3 is processed to GLI3R by the proteasome / PcG protein complex / Regulation of PLK1 Activity at G2/M Transition / Neddylation / embryonic pattern specification / (E3-independent) E2 ubiquitin-conjugating enzyme / mitochondrion localization / establishment of spindle localization / embryonic cleavage / MHC class II antigen presentation / gap junction / flagellated sperm motility / embryonic brain development / regulation of epithelial cell proliferation / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / intermediate filament cytoskeleton / methyl-CpG binding / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination
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 / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Beta tubulin / 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 / 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 / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / SKP1/BTB/POZ domain superfamily / Ring finger / Cupredoxin / Zinc finger PHD-type profile. / Leucine-rich repeat / Zinc finger, PHD-finger / 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 / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / Tubulin beta-2B chain ...ADENOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-DIPHOSPHATE / NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / Tubulin beta-2B chain / 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: 4.2 Å
AuthorsLiu, S.X. / Xue, J.C. / Zhang, Y. / Liu, Y.S. / Gao, H.S. / Shen, E.Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070628 China
National Natural Science Foundation of China (NSFC)32271258 China
CitationJournal: Nature / Year: 2026
Title: Molecular basis of oocyte cytoplasmic lattice assembly.
Authors: Shuxian Liu / Yusong Liu / Junchao Xue / Zhenzhen Li / Yan Zhang / Bailun Li / Lidan Xu / Lili Li / Zhenzhen Yu / Hongtao Yu / Haishan Gao / En-Zhi Shen /
Abstract: Mammalian oocytes are filled with fibric structures called cytoplasmic lattice (CPL) that are essential for oocyte maturation and early embryonic development. CPL comprises subcortical maternal ...Mammalian oocytes are filled with fibric structures called cytoplasmic lattice (CPL) that are essential for oocyte maturation and early embryonic development. CPL comprises subcortical maternal complex (SCMC) and multiple components, including PADI6. Although it was first discovered in the 1960s, the molecular architecture and assembly mechanisms of CPL remain poorly understood. Here we present the cryo-electron microscopy structure of CPL isolated from mouse oocytes. Our analysis identified 14 constitutive protein subunits and revealed that CPL is composed of repeating units comprising U-shaped basket (UB) and adapter ring (AR) features, forming a filamentous architecture. The AR adopts a two-fold symmetric conformation, containing two NLRP4F, four SCMC and two ZBED3 subunits circularized via two distinct interaction clusters. The UB is anchored by PADI6, a didecamer composed of ten homodimers assembled by two back-to-back pentamers, each forming the lateral side of the UB. The underfoot base and up and down sides of the UB are formed by multiple central-symmetric assemblies (UBE2D3-UHRF1-NLRP14) and (TUBB2B-TUBB2A-FBXW24-SKP1), respectively, associating with the PADI6 pentamers to construct the intact UB structure. Two SCMC dimers within each AR connect the up and down sides of two adjacent UBs with an extensive protein-protein interaction network, and thus maintain the repetitive connection between the neighbouring CPL units. Our work unveils the architectural principles underlying the assembly of this large, periodic CPL filament, offering a molecular basis for understanding the functions of CPL in early mammalian embryogenesis and female reproductive disorders.
History
DepositionJul 28, 2025Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Inactive protein-arginine deiminase type-6
C: Oocyte-expressed protein homolog
D: KH domain-containing protein 3
E: NLR family, pyrin domain containing 4F
H: Oocyte-expressed protein homolog
I: NLR family, pyrin domain containing 4F
J: FBXW24
K: S-phase kinase-associated protein 1
O: Ubiquitin-conjugating enzyme E2 D3
Q: E3 ubiquitin-protein ligase UHRF1
R: Zinc finger BED domain-containing protein 3
Z: Inactive protein-arginine deiminase type-6
c: Oocyte-expressed protein homolog
d: KH domain-containing protein 3
e: NLR family, pyrin domain containing 4F
h: Oocyte-expressed protein homolog
i: NLR family, pyrin domain containing 4F
j: FBXW24
k: S-phase kinase-associated protein 1
o: Ubiquitin-conjugating enzyme E2 D3
q: E3 ubiquitin-protein ligase UHRF1
r: Zinc finger BED domain-containing protein 3
z: Inactive protein-arginine deiminase type-6
2: Inactive protein-arginine deiminase type-6
3: Inactive protein-arginine deiminase type-6
4: Inactive protein-arginine deiminase type-6
5: Inactive protein-arginine deiminase type-6
6: Inactive protein-arginine deiminase type-6
7: Inactive protein-arginine deiminase type-6
8: Inactive protein-arginine deiminase type-6
9: Inactive protein-arginine deiminase type-6
12: Inactive protein-arginine deiminase type-6
N: NACHT, LRR and PYD domains-containing protein 14
P: E3 ubiquitin-protein ligase UHRF1
L: Tubulin beta-2A chain
M: Tubulin beta-2B chain
A: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
B: Transducin-like enhancer protein 6
F: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
G: Transducin-like enhancer protein 6
n: NACHT, LRR and PYD domains-containing protein 14
p: E3 ubiquitin-protein ligase UHRF1
l: Tubulin beta-2A chain
m: Tubulin beta-2B chain
a: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
b: Transducin-like enhancer protein 6
f: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
g: Transducin-like enhancer protein 6
11: Inactive protein-arginine deiminase type-6
19: Inactive protein-arginine deiminase type-6
15: Inactive protein-arginine deiminase type-6
16: Inactive protein-arginine deiminase type-6
14: Inactive protein-arginine deiminase type-6
13: Inactive protein-arginine deiminase type-6
17: Inactive protein-arginine deiminase type-6
18: Inactive protein-arginine deiminase type-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,656,58364
Polymers3,653,10156
Non-polymers3,4828
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 12 types, 52 molecules 1Zz23456789121119151614131718CHchDdEIei...

#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.: 20 / 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: 14294.582 Da / Num. of mol.: 4 / 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: 15250.954 Da / Num. of mol.: 2 / 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: 107564.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#5: Protein FBXW24


Mass: 53469.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#6: 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
#7: 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
#8: 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.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase
#9: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 6370.292 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#10: Protein NACHT, LRR and PYD domains-containing protein 14 / NALP-iota / Germ cell specific leucine-rich repeat NTPase


Mass: 110368.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6B966
#13: Protein
Isoform 4 of NACHT, LRR and PYD domains-containing protein 5 / Maternal antigen that embryos require / Mater protein / Ooplasm-specific protein 1 / OP1


Mass: 109296.773 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1M5
#14: Protein
Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 49005.340 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WVB3

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Tubulin beta- ... , 2 types, 4 molecules LlMm

#11: Protein Tubulin beta-2A chain


Mass: 49953.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q7TMM9
#12: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWF2

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Non-polymers , 2 types, 8 molecules

#15: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#16: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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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: mouse oocyte cytoplasmic lattices (CPL) / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL
Molecular weightValue: 2 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419:model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 676923 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003239117
ELECTRON MICROSCOPYf_angle_d0.625323918
ELECTRON MICROSCOPYf_dihedral_angle_d5.27131542
ELECTRON MICROSCOPYf_chiral_restr0.04436426
ELECTRON MICROSCOPYf_plane_restr0.00441567

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