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Yorodumi- PDB-9w2m: Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte -
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Open data
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Basic information
| Entry | Database: PDB / ID: 9w2m | |||||||||||||||||||||||||||
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| Title | Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte | |||||||||||||||||||||||||||
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Keywords | STRUCTURAL PROTEIN / Cytoplasmic lattice / Maternal complex / Cryo-EM structure / Protein assembly | |||||||||||||||||||||||||||
| Function / homology | Function and homology informationregulation 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 / F-box domain binding / Hedgehog 'off' state / RHO GTPases Activate Formins / Downstream TCR signaling / Separation of Sister Chromatids / Recruitment of NuMA to mitotic centrosomes / 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 / embryonic brain development / gap junction / establishment of spindle localization / (E3-independent) E2 ubiquitin-conjugating enzyme / mitochondrion localization / maintenance of protein location in nucleus / positive regulation of epithelial cell apoptotic process / Cul7-RING ubiquitin ligase complex Similarity search - Function | |||||||||||||||||||||||||||
| Biological species | ![]() | |||||||||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||||||||||||||||||||
Authors | Liu, S.X. / Xue, J.C. / Zhang, Y. / Liu, Y.S. / Gao, H.S. / Shen, E.Z. | |||||||||||||||||||||||||||
| Funding support | China, 2items
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Citation | Journal: Nature / Year: 2026Title: 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. | |||||||||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9w2m.cif.gz | 4.9 MB | Display | PDBx/mmCIF format |
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| PDB format | pdb9w2m.ent.gz | Display | PDB format | |
| PDBx/mmJSON format | 9w2m.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/9w2m ftp://data.pdbj.org/pub/pdb/validation_reports/w2/9w2m | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 65575MC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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| 1 |
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Components
-Protein , 12 types, 52 molecules 1Zz23456789121119151614131718CHchDdEIei...
| #1: Protein | Mass: 76854.109 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 14294.582 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 15250.954 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 107564.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 53469.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 18693.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #7: Protein | Mass: 16706.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P61079, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme #8: Protein | Mass: 88436.805 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase #9: Protein | Mass: 6370.292 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #10: Protein | Mass: 110368.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #13: Protein | Mass: 109296.773 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #14: Protein | Mass: 49005.340 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Tubulin beta- ... , 2 types, 4 molecules LlMm
| #11: Protein | Mass: 49953.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #12: Protein | Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 2 types, 8 molecules 


| #15: Chemical | ChemComp-GDP / #16: Chemical | ChemComp-ADP / |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | Y |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: mouse oocyte cytoplasmic lattices (CPL) / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL |
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| Molecular weight | Value: 2 MDa / Experimental value: NO |
| Source (natural) | Organism: ![]() |
| Buffer solution | pH: 7.5 |
| Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
| Specimen support | Grid type: Quantifoil R1.2/1.3 |
| Vitrification | Instrument: 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 |
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| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
| Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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| CTF correction | Type: NONE | ||||||||||||||||||||||||
| Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
| 3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 676923 / Symmetry type: POINT | ||||||||||||||||||||||||
| Refine LS restraints |
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FIELD EMISSION GUN