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- PDB-9sfp: Native cytoplasmic lattices from mouse oocytes -

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Basic information

Entry
Database: PDB / ID: 9sfp
TitleNative cytoplasmic lattices from mouse oocytes
Components
  • (NACHT, LRR and PYD domains-containing protein ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • F-box and WD-40 domain protein 12
  • Inactive protein-arginine deiminase type-6
  • KH domain-containing protein 3
  • NLR family, pyrin domain containing 4F
  • Oocyte-expressed protein homolog
  • Transducin-like enhancer protein 6
  • Tubulin alpha-1A chain
  • Tubulin beta-4B chain
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsSTRUCTURAL PROTEIN / oocyte / embryo / cytoskeleton / tubulin / ubiquitin
Function / homology
Function and homology information


regulation of translation by machinery localization / 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 ...regulation of translation by machinery localization / 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 / 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 / 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 / histone H3K23 ubiquitin ligase activity / COPI-mediated anterograde transport / spermatogonial cell division / Regulation of TNFR1 signaling / Kinesins / histone H3 reader activity / cortical granule / IKK complex recruitment mediated by RIP1 / 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 / Recycling pathway of L1 / 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 / axonemal microtubule / organelle transport along microtubule / 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 / Anchoring of the basal body to the plasma membrane / Separation of Sister Chromatids / Recruitment of NuMA to mitotic centrosomes / AURKA Activation by TPX2 / hemi-methylated DNA-binding / regulation of establishment of protein localization / forebrain morphogenesis / Peroxisomal protein import / cerebellar cortex morphogenesis / Regulation of PLK1 Activity at G2/M Transition / Neddylation / glial cell differentiation / neuron projection arborization / dentate gyrus development / embryonic pattern specification / (E3-independent) E2 ubiquitin-conjugating enzyme / mitochondrion localization / establishment of spindle localization / embryonic cleavage / MHC class II antigen presentation / flagellated sperm motility / regulation of epithelial cell proliferation / intermediate filament cytoskeleton / methyl-CpG binding / Antigen processing: Ubiquitination & Proteasome degradation / protein K11-linked ubiquitination / fertilization / protein K6-linked ubiquitination / pyramidal neuron differentiation / positive regulation of dendrite development / response to L-glutamate / epigenetic programming in the zygotic pronuclei / histone H3K9me2/3 reader activity / centrosome cycle / positive regulation of neurogenesis / 'de novo' protein folding / E2 ubiquitin-conjugating enzyme / tubulin complex / smoothened signaling pathway / mitotic spindle assembly checkpoint signaling / positive regulation of double-strand break repair / negative regulation of gene expression via chromosomal CpG island methylation
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. / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / A Receptor for Ubiquitination Targets / NOD2, winged helix domain / NOD2 winged helix domain / F-box domain profile. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / F-box-like / DAPIN domain / PAAD/DAPIN/Pyrin domain / F-box-like domain superfamily / PAAD/DAPIN/Pyrin domain / F-box domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / K Homology domain, type 1 superfamily / 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 / 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 / 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 / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1A chain / Tubulin beta-4B chain / F-box and WD-40 domain protein 12 / 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 ...NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1A chain / Tubulin beta-4B chain / F-box and WD-40 domain protein 12 / 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 / Transducin-like enhancer protein 6
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKilic, Z.I. / van Loenhout, J. / Chaillet, M. / Noteborn, W.E.M. / Leung, M.R.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Other government Netherlands
CitationJournal: Nature / Year: 2026
Title: Cytoplasmic lattices are megadalton storage complexes in mammalian oocytes.
Authors: Zeynep Ilgın Kılıç / Joyce van Loenhout / Marten Chaillet / Robert M van Es / Paula Sobrevals Alcaraz / Harmjan R Vos / Willem E M Noteborn / Miguel Ricardo Leung /
Abstract: Mammalian oocytes store proteins for embryonic development on abundant structures called cytoplasmic lattices (CPLs). However, the mechanisms by which they achieve this are unclear, largely because ...Mammalian oocytes store proteins for embryonic development on abundant structures called cytoplasmic lattices (CPLs). However, the mechanisms by which they achieve this are unclear, largely because the molecular composition of the lattices themselves is unknown. Here we use cryo-electron microscopy and artificial intelligence-based modelling to reveal the molecular architecture and protein composition of native CPLs from mouse oocytes. We find that CPLs are formed by at least 13 different proteins that assemble into a megadalton-scale complex, including multiple copies of maternal effect factors such as PADI6 and the subcortical maternal complex. We show that proteins that are essential for early embryonic development are structural components of the CPLs, including the cytoskeletal proteins α-tubulin and β-tubulin, which are incorporated into CPLs as unpolymerized dimers, and an array of ubiquitination factors such as the epigenetic regulator and E3 ligase UHRF1, ubiquitin-conjugating E2 enzymes, and ubiquitin ligase substrate adapters. This represents an elegant molecular mechanism by which oocytes stockpile vital proteins through direct incorporation into highly stable supramolecular assemblies. Our findings provide a structural framework for understanding how disrupting stored maternal factors leads to infertility and developmental defects.
History
DepositionAug 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: F-box and WD-40 domain protein 12
B: F-box and WD-40 domain protein 12
C: KH domain-containing protein 3
D: NLR family, pyrin domain containing 4F
F: NLR family, pyrin domain containing 4F
H: NACHT, LRR and PYD domains-containing protein 5
I: NACHT, LRR and PYD domains-containing protein 5
J: NACHT, LRR and PYD domains-containing protein 14
K: Oocyte-expressed protein homolog
L: Oocyte-expressed protein homolog
M: Inactive protein-arginine deiminase type-6
N: Inactive protein-arginine deiminase type-6
O: Inactive protein-arginine deiminase type-6
P: Inactive protein-arginine deiminase type-6
Q: Inactive protein-arginine deiminase type-6
R: Inactive protein-arginine deiminase type-6
S: Inactive protein-arginine deiminase type-6
T: Inactive protein-arginine deiminase type-6
U: Inactive protein-arginine deiminase type-6
V: Inactive protein-arginine deiminase type-6
W: Transducin-like enhancer protein 6
Y: Transducin-like enhancer protein 6
a: Tubulin alpha-1A chain
b: Tubulin beta-4B chain
c: Ubiquitin-conjugating enzyme E2 D3
d: E3 ubiquitin-protein ligase UHRF1
e: Zinc finger BED domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)1,915,32627
Polymers1,915,32627
Non-polymers00
Water00
1
A: F-box and WD-40 domain protein 12
B: F-box and WD-40 domain protein 12
C: KH domain-containing protein 3
D: NLR family, pyrin domain containing 4F
F: NLR family, pyrin domain containing 4F
H: NACHT, LRR and PYD domains-containing protein 5
I: NACHT, LRR and PYD domains-containing protein 5
J: NACHT, LRR and PYD domains-containing protein 14
K: Oocyte-expressed protein homolog
L: Oocyte-expressed protein homolog
M: Inactive protein-arginine deiminase type-6
N: Inactive protein-arginine deiminase type-6
O: Inactive protein-arginine deiminase type-6
P: Inactive protein-arginine deiminase type-6
Q: Inactive protein-arginine deiminase type-6
R: Inactive protein-arginine deiminase type-6
S: Inactive protein-arginine deiminase type-6
T: Inactive protein-arginine deiminase type-6
U: Inactive protein-arginine deiminase type-6
V: Inactive protein-arginine deiminase type-6
W: Transducin-like enhancer protein 6
Y: Transducin-like enhancer protein 6
a: Tubulin alpha-1A chain
b: Tubulin beta-4B chain
c: Ubiquitin-conjugating enzyme E2 D3
d: E3 ubiquitin-protein ligase UHRF1
e: Zinc finger BED domain-containing protein 3

A: F-box and WD-40 domain protein 12
B: F-box and WD-40 domain protein 12
C: KH domain-containing protein 3
D: NLR family, pyrin domain containing 4F
F: NLR family, pyrin domain containing 4F
H: NACHT, LRR and PYD domains-containing protein 5
I: NACHT, LRR and PYD domains-containing protein 5
J: NACHT, LRR and PYD domains-containing protein 14
K: Oocyte-expressed protein homolog
L: Oocyte-expressed protein homolog
M: Inactive protein-arginine deiminase type-6
N: Inactive protein-arginine deiminase type-6
O: Inactive protein-arginine deiminase type-6
P: Inactive protein-arginine deiminase type-6
Q: Inactive protein-arginine deiminase type-6
R: Inactive protein-arginine deiminase type-6
S: Inactive protein-arginine deiminase type-6
T: Inactive protein-arginine deiminase type-6
U: Inactive protein-arginine deiminase type-6
V: Inactive protein-arginine deiminase type-6
W: Transducin-like enhancer protein 6
Y: Transducin-like enhancer protein 6
a: Tubulin alpha-1A chain
b: Tubulin beta-4B chain
c: Ubiquitin-conjugating enzyme E2 D3
d: E3 ubiquitin-protein ligase UHRF1
e: Zinc finger BED domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)3,830,65354
Polymers3,830,65354
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1

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Components

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Protein , 11 types, 24 molecules ABCDFKLMNOPQRSTUVWYabcde

#1: Protein F-box and WD-40 domain protein 12 / F-box and WD-40 domain protein 20


Mass: 54036.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q5U467
#2: 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
#3: 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 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
#7: 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
#8: 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
#9: Protein Tubulin alpha-1A chain / Alpha-tubulin 1 / Alpha-tubulin isotype M-alpha-1 / Tubulin alpha-1 chain


Mass: 50188.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68369, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#10: 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
#11: 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
#12: 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
#13: 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

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

#4: 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
#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

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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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: native cytoplasmic lattices from mouse oocytes / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE-PROPANE

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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 magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
9PHENIX1.21.2_5419model refinement
10cryoSPARCinitial Euler assignment
11RELION5final Euler assignment
12RELION5classification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 424595 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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