EMDB-54838: Native cytoplasmic lattices from mouse oocytes

Basic information

Entry

Database: EMDB / ID: EMD-54838

• Title: Native cytoplasmic lattices from mouse oocytes
• Map data: composite map representing one globular repeat, locscale sharpened

Sample

• Complex: native cytoplasmic lattices from mouse oocytes
  • Protein or peptide: x 13 types

• Keywords: oocyte / embryo / cytoskeleton / tubulin / ubiquitin / STRUCTURAL PROTEIN

Function / homology

Function:

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

Domain/homology:

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

Component:

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

• Biological species: Mus musculus (house mouse)
• Method: single particle reconstruction / cryo EM / Resolution: 4.2 Å
• Authors: Kilic ZI / van Loenhout J / Chaillet M / Noteborn WEM / Leung MR

Funding support

Netherlands, 1 items

Organization	Grant number	Country
Other government		Netherlands

• Citation: Journal: To Be Published; Title: Maternal factors assemble into megadalton storage complexes in mammalian oocytes; Authors: Kilic ZI / van Loenhout J / Chaillet M / Noteborn WEM / Leung MR

History

Deposition	Aug 20, 2025	-
Header (metadata) release	Mar 18, 2026	-
Map release	Mar 18, 2026	-
Update	Mar 18, 2026	-
Current status	Mar 18, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_54838.map.gz / Format: CCP4 / Size: 747.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: composite map representing one globular repeat, locscale sharpened
• Voxel size: X=Y=Z: 1.06 Å

Density

Contour Level	By AUTHOR: 0.1
Minimum - Maximum	0.0 - 0.43751198
Average (Standard dev.)	0.0021760138 (±0.016178144)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin -71 -1 -5 Dimensions 584 645 520 Spacing 645 584 520
Cell	A: 683.69995 Å / B: 619.04 Å / C: 551.19995 Å α=β=γ: 90.0 °

Supplemental data

Additional map: composite map representing one asymmetric unit, locscale sharpened

• File: emd_54838_additional_1.map
• Annotation: composite map representing one asymmetric unit, locscale sharpened

Sample components

Entire : native cytoplasmic lattices from mouse oocytes

• Entire: Name: native cytoplasmic lattices from mouse oocytes

Components

• Complex: native cytoplasmic lattices from mouse oocytes
  • Protein or peptide: F-box and WD-40 domain protein 12
  • Protein or peptide: KH domain-containing protein 3
  • Protein or peptide: NLR family, pyrin domain containing 4F
  • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
  • Protein or peptide: NACHT, LRR and PYD domains-containing protein 14
  • Protein or peptide: Oocyte-expressed protein homolog
  • Protein or peptide: Inactive protein-arginine deiminase type-6
  • Protein or peptide: Transducin-like enhancer protein 6
  • Protein or peptide: Tubulin alpha-1A chain
  • Protein or peptide: Tubulin beta-4B chain
  • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
  • Protein or peptide: E3 ubiquitin-protein ligase UHRF1
  • Protein or peptide: Zinc finger BED domain-containing protein 3

Supramolecule #1: native cytoplasmic lattices from mouse oocytes

• Supramolecule: Name: native cytoplasmic lattices from mouse oocytes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Mus musculus (house mouse)

Macromolecule #1: F-box and WD-40 domain protein 12

• Macromolecule: Name: F-box and WD-40 domain protein 12 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 54.036707 KDa

Sequence

String:

MEVHLPRLPL MKIFSYLDAY SLLQAAQVNK NWNELASSDV LWRKLCQKRW LFCDMVTLQL LGTETWKQFF VFRTWQEHAK TRAKPEDFT YKEIPAEYGF RANACYISGC GLTRNVQDRS VICMVSSMTK LSTWDIREGI MTWVSTEQPA YIKLLTTLPE M HIAVTVDT HSTIKLWDCH NREALATNCL FSSCKLLKAV FSKDDPIVLV GDISGNLYIF RIPDLHLISK VNVFPYGIDE LH CSPQKKW VFLIMKHPRV LTKVVYMNSL LRTSEFSAPV STILKFSLCD KAFWTPRRED RITQMSRGVP PRPTKFATFD MKL EEIGNK VTVQEYLVAS FSLQDYEASP EWMGVSNKDV IVCSTGSSLL LFNIHGLRLQ TFHYCPEEIL RLWVDPLHVI VTCN DGSMD VYAWEERSLL LRKCYRLQNR RNLPPESFIF KTLCDDVSII GVMTNSPAPC FLMAYTLASA LEN

UniProtKB: F-box and WD-40 domain protein 12

Macromolecule #2: KH domain-containing protein 3

• Macromolecule: Name: KH domain-containing protein 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 48.055301 KDa

Sequence

String:

MASLKRFQTL VPLDHKQGTL FEIIGEPKLP KWFHVECLED PKRLYVEPRL LEIMFGKDGE HIPHLESMLH TLIHVNVWGP ERRAEIWIF GPPPFRRDVD RMLTDLAHYC RMKLMEIEAL EAGVERRRMA AHKAATQPAP VKVREAAPRP ASVKVPETAT Q PAPVKVRE AAPQPAPVQE VREAAPQQAS VQEEVREAAT EQAPVQEVRE AATEQAPVQE VSEAATEQAP VQEVNEAATE QA SVQAVRE AATRPAPGKV RKAATQPAPV QVCQEATQLA PVKVREAATQ PASGKVREAA TQLAPVKVRK AATQLAPVKV HEA ATQPAP GKVSDAATQS ASVQVREAAT QLSPVEATDT SQLAQVKADE AFAQHTSGEA HQVANGQSPI EVCETATGQH SLDV SRALS QKCPEVFEWE TQSCLDGSYV IVQPPRDAWE SFIIL

UniProtKB: KH domain-containing protein 3

Macromolecule #3: NLR family, pyrin domain containing 4F

• Macromolecule: Name: NLR family, pyrin domain containing 4F / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 108.001281 KDa

Sequence

String:

MASFISDFGL IWYLRELNKK EFMKFKDFLI QEILELKLKQ VSSTKVKKAS REDLANLLLK CGENQAWDMT FRILQKINRK DLTERATGA IVGNPNLYRD HLKKKLTHDC PKKFNVRIQD FIKETFIQND YDAFENLLIS KGTERKPHMV FLKGMAGVGK T LMLKNLML AWSKGLVFQN KFSYAFYFCC QDVKQLKTAS LAELISREWP SPSAPIEEIL SQPEKLLFII DSLEGMEWDL TK QESELCD DCMEKQPVST LLSSLLRRKM LPESSLLLST TPETFEKMED RIQCTDVKTA TAFDERSMKI YFHRLFQDRK RAQ EAFSLV RENKQLFTIC QVPLLCWMVA TCLKEEIEKG GDPVSLCRRT TSLYTTHIFS LFIPQSAQYP SKKSQDQLQG LCSL AAEGM WTDTFVFGKE ALRRNGIFDS DIPTLLDIGM LGKIREFENS YIFLHPSVQE VCAAIFYMLK RHVEHPSQDV KNIET VLFM FLKKVKTQWI FLGCFIFGLL QKSEQEKLGV FFGHRLSKNI HHKLYQCLET LSGNAELQEQ IDGMRLFSCL FEMEDE AFL VKAMNCMQQI NFVAKNYSDF IVAAYCLKHC STLKKLSFST ENVLNEGDQS YMEELLICWN NMCSVFVRSK DIQELRI KD TNFNEPAIRV LYESLKYPSF TLNKLVANNV SFGDNHVLFE LIQNSSLQYL DLSCSFLSHN EVKLLCDILN QAECNIEK L MIAHCKLSPD DCKIFGSILM SSKSLKVLNL ASNNLNQGIS SLCKALCHPH CTLEYLVLSN CSLSEQCWDY LSEVLRQNK TLSHLDISSN DLKDEGLKIL CRSLILPYCV LESLCLSCCG ITERGCQDLA EVLKNNQNLK YLHVSYNKLK DTGVMLLCDA IKHPNCHLK DLQLEACEIT DASNEELCYA FMQCETLQTL NLMGNAFEVS RMVFFPRF

UniProtKB: NLR family, pyrin domain containing 4F

Macromolecule #4: NACHT, LRR and PYD domains-containing protein 5

• Macromolecule: Name: NACHT, LRR and PYD domains-containing protein 5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 131.468547 KDa

Sequence

String:

MGPPEKESKA ILKARGLEEE QKSERKMTSP ENDSKSIQKD QGPEQEQTSE STMGPPEKES KAILKARGLE EEQKSERKMT SPENDSKSI QKDQGPEQEQ TSESTMGPPE KDSKAILKAR GLEEEQKSES TMSPSENVSR AILKDSGSEE VEQASERKMT S PENDSKSI QKDQGPEQEQ TSETLQSKEE DEVTEADKDN GGDLQDYKAH VIAKFDTSVD LHYDSPEMKL LSDAFKPYQK TF QPHTIIL HGRPGVGKSA LARSIVLGWA QGKLFQKMSF VIFFSVREIK WTEKSSLAQL IAKECPDSWD LVTKIMSQPE RLL FVIDGL DDMDSVLQHD DMTLSRDWKD EQPIYILMYS LLRKALLPQS FLIITTRNTG LEKLKSMVVS PLYILVEGLS ASRR SQLVL ENISNESDRI QVFHSLIENH QLFDQCQAPS VCSLVCEALQ LQKKLGKRCT LPCQTLTGLY ATLVFHQLTL KRPSQ SALS QEEQITLVGL CMMAAEGVWT MRSVFYDDDL KNYSLKESEI LALFHMNILL QVGHNSEQCY VFSHLSLQDF FAALYY VLE GLEEWNQHFC FIENQRSIME VKRTDDTRLL GMKRFLFGLM NKDILKTLEV LFEYPVIPTV EQKLQHWVSL IAQQVNG TS PMDTLDAFYC LFESQDEEFV GGALKRFQEV WLLINQKMDL KVSSYCLKHC QNLKAIRVDI RDLLSVDNTL ELCPVVTV Q ETQCKPLLME WWGNFCSVLG SLRNLKELDL GDSILSQRAM KILCLELRNQ SCRIQKLTFK SAEVVSGLKH LWKLLFSNQ NLKYLNLGNT PMKDDDMKLA CEALKHPKCS VETLRLDSCE LTIIGYEMIS TLLISTTRLK CLSLAKNRVG VKSMISLGNA LSSSMCLLQ KLILDNCGLT PASCHLLVSA LFSNQNLTHL CLSNNSLGTE GVQQLCQFLR NPECALQRLI LNHCNIVDDA Y GFLAMRLA NNTKLTHLSL TMNPVGDGAM KLLCEALKEP TCYLQELELV DCQLTQNCCE DLACMITTTK HLKSLDLGNN AL GDKGVIT LCEGLKQSSS SLRRLGLGAC KLTSNCCEAL SLAISCNPHL NSLNLVKNDF STSGMLKLCS AFQCPVSNLG IIG LWKQEY YARVRRQLEE VEFVKPHVVI DGDWYASDED DRNWWKN

UniProtKB: NACHT, LRR and PYD domains-containing protein 5

Macromolecule #5: NACHT, LRR and PYD domains-containing protein 14

• Macromolecule: Name: NACHT, LRR and PYD domains-containing protein 14 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 113.527188 KDa

Sequence

String:

MKTEDDEMEY EASKEETVSE DKDFDDGIDY RTVIKENIFT MWYKTSLHGE FATLNCVITP KDQNLLQHIF DEDIQTSEAP QTVVLQGAA GIGKTTLLKK AVLEWADGNL YQQFTHVFYL NGKEISQVKE KSFAQLISKH WPSSEGPIEQ VLSKPSSLLF I IDSFDELD FSFEEPQFAL CKDWTQISPV SFLISSLLRK VMLPESYLLV ATRSTAWKRL VPLLQKPQRV KLSGLSKNAR MD YIHHLLK DKAWATSAIY SLRMNWRLFH MCHVCHMCQM ICAVLKGQVE KGGRVEETCK TSTALFTYYI CSLFPRIPVG CVT LPNETL LRSLCKAAVE GIWTMKHVLY QQNLRKHELT REDILLFLDA KVLQQDTEYE NCYMFTHLHV QEFFAALFYL LREN LEEQD YPSEPFENLY LLLESNHIHD PHLEQMKCFL FGLLNKDRVR QLEETFNLTI SMEVREELLA CLEGLEKDDS SLSQL RFQD LLHCIYETQD QEFITQALMY FQKIIVRVDE EPQLRIYSFC LKHCHTLKTM RLTARADLKN MLDTAEMCLE GAAVQV IHY WQDLFSVLHT NESLIEMDLY ESRLDESLMK ILNEELSHPK CKLQKLIFRA VDFLNGCQDF TFLASNKKVT HLDLKET DL GVNGLKTLCE ALKCKGCKLR VLRLASCDLN VARCQKLSNA LQTNRSLVFL NLSLNNLSND GVKSLCEVLE NPNSSLER L ALASCGLTKA GCKVLSSALT KSKRLTHLCL SDNVLEDEGI KLLSHTLKHP QCTLQSLVLR SCSFTPIGSE HLSTALLHN RSLVHLDLGQ NKLADNGVKL LCHSLQQPHC NLQELELMSC VLTSKACGDL ASVLVNNSNL WSLDLGHNIL DDAGLNILCD ALRNPNCHV QRLGLENCGL TPGCCQDLLG ILSNNKSVIQ MNLMKNALDH ESIKNLCKVL RSPTCKMEFL ALDKKEILKK K IKKFLVDV RINNPHLVIG PECPNTESGC WWNYF

UniProtKB: NACHT, LRR and PYD domains-containing protein 14

Macromolecule #6: Oocyte-expressed protein homolog

• Macromolecule: Name: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 18.481295 KDa

Sequence

String:

MASHTADADA KPDSDSQKLL NVLPVSLRLR TRPWWFPIQE VSNPLVLYME AWVAERVIGT DQAEISEIEW MCQALLTVDS VNSGNLAEI TIFGQPSAQT RMKNILLNMA AWHKENELQR AVKVKEVEEF LKIRASSILS KLSKKGLKLA GFPLPLEGRE T QMES

UniProtKB: Oocyte-expressed protein homolog

Macromolecule #7: Inactive protein-arginine deiminase type-6

• Macromolecule: Name: Inactive protein-arginine deiminase type-6 / type: protein_or_peptide / ID: 7 / Number of copies: 10 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 76.854109 KDa

Sequence

String:

MSFQNSLSLS LVNPTHALCM VGMEITLDIS KCAPDKCKSF TIRGSPRILI HISSSVIAGK EDTVVWRSMN HPTVALVRMV APSPTVDED KVLVSYFCPD QEVPTATAVL FLTGIEISLE ADIYRDGQLD MPSDKQAKKK WMWGMNGWGA ILLVNCSPNA V GQPDEQSF QEGPREIQNL SQMNVTVEGP TSILQNYQLI LHTSEEEAKK TRVYWSQRGS SAYELVVGPN KPVYLLPTFE NR RKEAFYV EATEFPSPSF SGLISLSLSL VEKAHDECIP EIPLYKDTVM FRVAPYIFMP STQMPLEVYL CRELQLQGFV DSV TKLSEK SKVQVVKVYE DPNRQSKWLQ DEMAFCYTQA PHKTVSLILD TPRVSKLEDF PMKYTLTPGS GYLIRQTEDH RVAS LDSIG NLMVSPPVKA QGKDYPLGRV LIGGSFYPSS EGRDMNKGLR EFVYAQQVQA PVELFSDWLM TGHMDQFMCF VPTND KNND QKDFRLLLAS PSACFELFEQ KQKEGYGNVT LFEDIGAEQL LSNGRESKTI SQILADKSFR EQNTYVEKCI SLNRTL LKT ELGLEDKDII LIPQLFCLEQ LTNVPSNQQS TKLFARPYFP DMLQIIVLGK NLGIPKPFGP KINGTCCLEE KVCGLLE PL GLKCTFIDDF DCYLANIGDV CASAIINRVP FAFKWWKMTP

UniProtKB: Inactive protein-arginine deiminase type-6

Macromolecule #8: Transducin-like enhancer protein 6

• Macromolecule: Name: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 65.187332 KDa

Sequence

String:

MTSHRQSSDT FGGILPSTLS SRYLSIVNQL PEEFSSVVSE MMVHLENIFS LAENFFQAIE RFSRTPDLLE RNKMSIGVGA EGDSWPCHV SHEAPMGSAQ TTENSAKEED KQVPESAALQ HPKFKSTPGP QLPTRRRFLS ESDELQDPQP VWDAEPQFCQ G FLIQGLWE LFMDSRQKNQ QEHGGEDSSQ ESKDSGLCDF KPEPQPRHRN SLSDSADPFL IKSPSALLDY YQEDVSRPQP ET QESSGRA DKFLKPLSWG SEVLESSCNQ PSTALWQLER FTVPQALQKV RVLKHQELLL VVAVSSFTRH VFTCSQSGIK VWN LVNQVA EDRDPESHLK CSVQDNKVYL RTCLLSSNSR TLFAGGYNLP GVIVWDLAAP SLYEKCQLPC EGLSCQALAN TKEN MALAG FTDGTVRIWD LRTQEIVRNL KGPTNSARNL VVKDDNIWTG GLDACLRCWD LRMAKVSLEH LFQSQIMSLA HSPTE DWLL LGLANGQHCL FNSRKRDQVL TVDTKDNTIL GLKFSPNGKW WASVGMGNFI TVHSMPTGAK LFQVPEVGPV RCFDMT ENG RLIITGSRDC ASVYHIKY

UniProtKB: Transducin-like enhancer protein 6

Macromolecule #9: Tubulin alpha-1A chain

• Macromolecule: Name: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO; EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 50.188441 KDa

Sequence

String:

MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1A chain

Macromolecule #10: Tubulin beta-4B chain

• Macromolecule: Name: Tubulin beta-4B chain / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 49.877824 KDa

Sequence

String:

MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE FEEEAEEEVA

UniProtKB: Tubulin beta-4B chain

Macromolecule #11: Ubiquitin-conjugating enzyme E2 D3

• Macromolecule: Name: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 16.706133 KDa

Sequence

String:

MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DRDKYNRISR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D3

Macromolecule #12: E3 ubiquitin-protein ligase UHRF1

• Macromolecule: Name: E3 ubiquitin-protein ligase UHRF1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 88.436805 KDa

Sequence

String:

MWIQVRTMDG KETHTVNSLS RLTKVQELRK KIEEVFHVEP QLQRLFYRGK QMEDGHTLFD YDVRLNDTIQ LLVRQSLALP LSTKERDSE LSDSDSGYGV GHSESDKSST HGEGAAEADD KTVWEDTDLG LYKVNEYVDV RDNIFGAWFE AQVVQVQKRA L SEDEPCSS SAVKTSEDDI MYHVKYDDYP EHGVDIVKAK NVRARARTVI PWENLEVGQV VMANYNVDYP RKRGFWYDVE IC RKRQTRT ARELYGNIRL LNDSQLNNCR IMFVDEVLMI ELPKERRPLI ASPSQPPPAL RNTGKSGPSC RFCKDDENKP CRK CACHVC GGREAPEKQL LCDECDMAFH LYCLKPPLTS VPPEPEWYCP SCRTDSSEVV QAGEKLKESK KKAKMASATS SSRR DWGKG MACVGRTTEC TIVPANHFGP IPGVPVGTMW RFRVQVSESG VHRPHVAGIH GRSNDGAYSL VLAGGYEDDV DNGNY FTYT GSGGRDLSGN KRTAGQSSDQ KLTNNNRALA LNCHSPINEK GAEAEDWRQG KPVRVVRNMK GGKHSKYAPA EGNRYD GIY KVVKYWPERG KSGFLVWRYL LRRDDTEPEP WTREGKDRTR QLGLTMQYPE GYLEALANKE KSRKRPAKAL EQGPSSS KT GKSKQKSTGP TLSSPRASKK SKLEPYTLSE QQANLIKEDK GNAKLWDDVL TSLQDGPYQI FLSKVKEAFQ CICCQELV F RPVTTVCQHN VCKDCLDRSF RAQVFSCPAC RFELDHSSPT RVNQPLQTIL NQLFPGYGSG R

UniProtKB: E3 ubiquitin-protein ligase UHRF1

Macromolecule #13: Zinc finger BED domain-containing protein 3

• Macromolecule: Name: Zinc finger BED domain-containing protein 3 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 25.643373 KDa

Sequence

String:

MKSKKPLKIT MEDSRRLNDP AEQGGLCPAP VGPSYSEAWG YFHLDPAQPR HRMMSAWATC RLCGLQVGGL PNFQMWTRAL CQHLSDVHL PELKKSAAPS SPTTMPCPPP PSPTMAAEGD WARLLEQMGE LAMRGSQREL ELERREAALM QAELELERKR Q ALKQEAQS VEQERHQLQV EREALSKWIK KQSPGAQVPE PPSPLPLLPK EDPDIHDNNS DNDMVTKVLL

UniProtKB: Zinc finger BED domain-containing protein 3

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 7.2
• Grid: Model: Quantifoil R2/1 / Material: COPPER
• Vitrification: Cryogen name: ETHANE-PROPANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 81000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Software - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

Startup model

Type of model: EMDB MAP
EMDB ID:

16458

• Final reconstruction: Applied symmetry - Point group: C₂ (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 424595
• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5)
• Final 3D classification: Software - Name: RELION (ver. 5)

Atomic model buiding 1

• Refinement: Protocol: FLEXIBLE FIT

Output model

PDB-9sfp:
Native cytoplasmic lattices from mouse oocytes