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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 / ooplasm / cortical granule exocytosis / embryonic process involved in female pregnancy / endoplasmic reticulum localization / Carboxyterminal post-translational modifications of tubulin / SCF-beta-TrCP mediated degradation of Emi1 / Intraflagellar transport / establishment or maintenance of apical/basal cell polarity / E3 ubiquitin ligases ubiquitinate target proteins / Downregulation of SMAD2/3:SMAD4 transcriptional activity / COPI-independent Golgi-to-ER retrograde traffic / Regulation of BACH1 activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / SCF(Skp2)-mediated degradation of p27/p21 / cytoplasm organization / MAP3K8 (TPL2)-dependent MAPK1/3 activation / histone H3K18 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / Regulation of TNFR1 signaling / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of RUNX2 expression and activity / histone H3K23 ubiquitin ligase activity / Degradation of GLI1 by the proteasome / COPI-mediated anterograde transport / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / spermatogonial cell division / 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 / Kinesins / Aggrephagy / cortical granule / histone H3 reader activity / PKR-mediated signaling / 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 / RHO GTPases activate IQGAPs / Iron uptake and transport / Activation of NF-kappaB in B cells / The role of GTSE1 in G2/M progression after G2 checkpoint / Recycling pathway of L1 / COPI-dependent Golgi-to-ER retrograde traffic / FCERI mediated NF-kB activation / apical cortex / positive regulation of meiotic nuclear division / CLEC7A (Dectin-1) signaling / chromosomal DNA methylation maintenance following DNA replication / Interleukin-1 signaling / RHO GTPases Activate Formins / regulation of RNA stability / positive regulation of embryonic development / Separation of Sister Chromatids / Downstream TCR signaling / Hedgehog 'off' state / F-box domain binding / Recruitment of NuMA to mitotic centrosomes / regulation of establishment of protein localization / Peroxisomal protein import / hemi-methylated DNA-binding / GLI3 is processed to GLI3R by the proteasome / PcG protein complex / Regulation of PLK1 Activity at G2/M Transition / Neddylation / embryonic pattern specification / embryonic cleavage / (E3-independent) E2 ubiquitin-conjugating enzyme / mitochondrion localization / embryonic brain development / establishment of spindle localization / MHC class II antigen presentation / gap junction / flagellated sperm motility / regulation of epithelial cell proliferation / maintenance of protein location in nucleus / Cul7-RING ubiquitin ligase complex / intermediate filament cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / methyl-CpG binding / 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 / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / PAAD/DAPIN/Pyrin 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 / Tubulin / Death-like domain superfamily / 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 / Ring finger / SKP1/BTB/POZ domain superfamily / 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: To Be Published
Title: Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte
Authors: Liu, S.X. / Xue, J.C. / Zhang, Y. / Liu, Y.S. / Gao, H.S. / Shen, E.Z.
History
DepositionJul 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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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