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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 / E3 ubiquitin ligases ubiquitinate target proteins / endoplasmic reticulum localization / Carboxyterminal post-translational modifications of tubulin / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Intraflagellar transport / establishment or maintenance of apical/basal cell polarity / ooplasm / COPI-independent Golgi-to-ER retrograde traffic / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Regulation of TNFR1 signaling / cytoplasm organization / histone H3 ubiquitin ligase activity / IKK complex recruitment mediated by RIP1 / COPI-mediated anterograde transport / Aggrephagy / spermatogonial cell division / Kinesins / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cortical granule / Resolution of Sister Chromatid Cohesion / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / RHO GTPases activate IQGAPs / Recycling pathway of L1 / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / apical cortex / axonemal microtubule / positive regulation of meiotic nuclear division / Separation of Sister Chromatids / regulation of RNA stability / positive regulation of embryonic development / organelle transport along microtubule / Hedgehog 'off' state / Peroxisomal protein import / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / hemi-methylated DNA-binding / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / regulation of establishment of protein localization / forebrain morphogenesis / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / cerebellar cortex morphogenesis / Neddylation / glial cell differentiation / dentate gyrus development / neuron projection arborization / embryonic pattern specification / (E3-independent) E2 ubiquitin-conjugating enzyme / MHC class II antigen presentation / embryonic cleavage / protein K6-linked ubiquitination / mitochondrion localization / flagellated sperm motility / establishment of spindle localization / regulation of epithelial cell proliferation / intermediate filament cytoskeleton / Antigen processing: Ubiquitination & Proteasome degradation / : / methyl-CpG binding / protein K11-linked ubiquitination / fertilization / histone H3K9me2/3 reader activity / pyramidal neuron differentiation / response to L-glutamate / epigenetic programming in the zygotic pronuclei / positive regulation of dendrite development / centrosome cycle / positive regulation of neurogenesis / 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 / regulation of synapse organization / startle response / exocytosis / motor behavior / microtubule polymerization / positive regulation of protein metabolic process
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 / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / F-box domain profile. / NACHT nucleoside triphosphatase / NACHT domain / F-box-like / NACHT-NTPase domain profile. / F-box-like domain superfamily / DAPIN domain / PAAD/DAPIN/Pyrin domain / 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 / Beta tubulin / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Death-like domain superfamily / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / 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: To Be Published
Title: Maternal factors assemble into megadalton storage complexes in mammalian oocytes
Authors: Kilic, Z.I. / van Loenhout, J. / Chaillet, M. / Noteborn, W.E.M. / Leung, M.R.
History
DepositionAug 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 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
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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