EMDB-76334: Native structure of the cytoplasmic lattice (CPL) asymmetric unit...

Basic information

Entry

Database: EMDB / ID: EMD-76334

• Title: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs

Sample

• Complex: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
  • Protein or peptide: x 16 types
• Ligand: x 4 types

• Keywords: cytoplasmic lattice / egg / filamentous assembly / CYTOSOLIC PROTEIN

Function / homology

Function:

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 / The role of GTSE1 in G2/M progression after G2 checkpoint / embryonic cleavage / apical cortex / Recycling pathway of L1 / positive regulation of meiotic nuclear division / chromosomal DNA methylation maintenance following DNA replication / positive regulation of embryonic development / regulation of RNA stability / intermediate filament cytoskeleton / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / axonemal microtubule / Hedgehog 'off' state / RHO GTPases Activate Formins / F-box domain binding / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Downstream TCR signaling / Separation of Sister Chromatids / Anchoring of the basal body to the plasma membrane / Recruitment of NuMA to mitotic centrosomes / AURKA Activation by TPX2 / 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 / gap junction / establishment of spindle localization

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 / F-box domain profile. / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / F-box-like / NACHT nucleoside triphosphatase / F-box-like domain superfamily / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / F-box 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 / 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. / 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 / SKP1/BTB/POZ domain 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 / Ring finger / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Cupredoxin / Tubulin/FtsZ, GTPase domain superfamily / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Leucine-rich repeat / 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

Component:

NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / F-box domain-containing protein / F-box domain-containing protein / 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 / S-phase kinase-associated protein 1 / Transducin-like enhancer protein 6

• Biological species: Mus musculus (house mouse)
• Method: single particle reconstruction / cryo EM / Resolution: 3.5 Å
• Authors: Li Y / Zheng W / Leem J / Wu C / Tang S / Mogessie B / Xiong Y

Funding support

United States, 1 items

Organization	Grant number	Country
Other government		United States

• Citation: Journal: Nat Struct Mol Biol / Year: 2026; Title: Cytoplasmic lattices store developmentally poised degradative and cytoskeletal complexes in mammalian eggs.; Authors: Yujie Li / Wei Zheng / Jiyeon Leem / Chunxiang Wu / Shaogeng Tang / Binyam Mogessie / Yong Xiong / ; Abstract: The cytoplasmic lattice (CPL) in mammalian eggs is essential for early embryonic development but its molecular components, structural organization and functional capacity have remained elusive. Here, using cryo-electron microscopy, we show that the CPL filament in mouse metaphase II eggs contains repeating units with a periodicity of ~37 nm and determine its high-resolution, native structure and complete subunit composition. The CPL architecture organizes maternal-effect proteins, ubiquitination machinery and tubulin into a highly structured reservoir. Maternal-effect proteins form the scaffold of the CPL to sequester a UHRF1-UBE2D3 E3-E2 ubiquitination module and three distinct FBXW-SKP1 E3 ubiquitin ligase components, notably all in activity-excluded states. The CPL further contains αβ-tubulin heterodimers in a GTP-bound state, indicating microtubule-assembly-competent tubulin held in reserve. CPL filaments are capped by a terminal unit that lacks a PADI6 dimer, a scaffold component, suggesting a structural mechanism that prevents further oligomerization. Interactions between neighboring CPL filaments promote the assembly of a three-dimensional network in the egg cytoplasm. Taken together, our work defines how CPL assembly and architecture prime mammalian eggs for ubiquitin-mediated protein degradation and cytoskeletal remodeling during the egg-to-embryo transition.

History

Deposition	Mar 29, 2026	-
Header (metadata) release	Apr 8, 2026	-
Map release	Apr 8, 2026	-
Update	Jul 29, 2026	-
Current status	Jul 29, 2026	Processing site: RCSB / Status: Released

Map

• File: Download / File: emd_76334.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.068 Å

Density

Contour Level	By AUTHOR: 0.1
Minimum - Maximum	0.0 - 2.7024968
Average (Standard dev.)	0.0035849316 (±0.031021673)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 512 512 512 Spacing 512 512 512
Cell	A=B=C: 546.816 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_76334_msk_1.map

Half map: #2

• File: emd_76334_half_map_1.map

Half map: #1

• File: emd_76334_half_map_2.map

Sample components

Entire : Native structure of the cytoplasmic lattice (CPL) asymmetric unit...

• Entire: Name: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs

Components

• Complex: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
  • Protein or peptide: Tubulin beta-4B chain
  • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
  • Protein or peptide: Oocyte-expressed protein homolog
  • Protein or peptide: Transducin-like enhancer protein 6
  • Protein or peptide: Zinc finger BED domain-containing protein 3
  • Protein or peptide: KH domain-containing protein 3
  • Protein or peptide: NLR family, pyrin domain containing 4F
  • Protein or peptide: Inactive protein-arginine deiminase type-6
  • Protein or peptide: Tubulin alpha-1C chain
  • Protein or peptide: NACHT, LRR and PYD domains-containing protein 14
  • Protein or peptide: E3 ubiquitin-protein ligase UHRF1
  • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
  • Protein or peptide: F-box and WD-40 domain protein 19
  • Protein or peptide: S-phase kinase-associated protein 1
  • Protein or peptide: Expressed sequence C85627
  • Protein or peptide: F-box and WD-40 domain protein 21
• Ligand: GUANOSINE-5'-TRIPHOSPHATE
• Ligand: MAGNESIUM ION
• Ligand: ZINC ION
• Ligand: CALCIUM ION

Supramolecule #1: Native structure of the cytoplasmic lattice (CPL) asymmetric unit...

• Supramolecule: Name: Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
• Source (natural): Organism: Mus musculus (house mouse)

Macromolecule #1: Tubulin beta-4B chain

• Macromolecule: Name: Tubulin beta-4B chain / type: protein_or_peptide / ID: 1 / 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 #2: NACHT, LRR and PYD domains-containing protein 5

• Macromolecule: Name: NACHT, LRR and PYD domains-containing protein 5 / type: protein_or_peptide / ID: 2 / 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 #3: Oocyte-expressed protein homolog

• Macromolecule: Name: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 3 / 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 #4: Transducin-like enhancer protein 6

• Macromolecule: Name: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 4 / 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 #5: Zinc finger BED domain-containing protein 3

• Macromolecule: Name: Zinc finger BED domain-containing protein 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 25.51218 KDa

Sequence

String:

KSKKPLKITM EDSRRLNDPA EQGGLCPAPV GPSYSEAWGY FHLDPAQPRH RMMSAWATCR LCGLQVGGLP NFQMWTRALC QHLSDVHLP ELKKSAAPSS PTTMPCPPPP SPTMAAEGDW ARLLEQMGEL AMRGSQRELE LERREAALMQ AELELERKRQ A LKQEAQSV EQERHQLQVE REALSKWIKK QSPGAQVPEP PSPLPLLPKE DPDIHDNNSD NDMVTKVLL

UniProtKB: Zinc finger BED domain-containing protein 3

Macromolecule #6: KH domain-containing protein 3

• Macromolecule: Name: KH domain-containing protein 3 / type: protein_or_peptide / ID: 6 / 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 #7: NLR family, pyrin domain containing 4F

• Macromolecule: Name: NLR family, pyrin domain containing 4F / type: protein_or_peptide / ID: 7 / Number of copies: 1 / 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 #8: Inactive protein-arginine deiminase type-6

• Macromolecule: Name: Inactive protein-arginine deiminase type-6 / type: protein_or_peptide / ID: 8 / 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 #9: Tubulin alpha-1C chain

• Macromolecule: Name: Tubulin alpha-1C 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: 49.962172 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 RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLT VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GADSAEGDDE GEEY

UniProtKB: Tubulin alpha-1C chain

Macromolecule #10: NACHT, LRR and PYD domains-containing protein 14

• Macromolecule: Name: NACHT, LRR and PYD domains-containing protein 14 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / 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 #11: E3 ubiquitin-protein ligase UHRF1

• Macromolecule: Name: E3 ubiquitin-protein ligase UHRF1 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / 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 #12: Ubiquitin-conjugating enzyme E2 D3

• Macromolecule: Name: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / 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 #13: F-box and WD-40 domain protein 19

• Macromolecule: Name: F-box and WD-40 domain protein 19 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 53.657457 KDa

Sequence

String:

MEIHLPSLPM MKILSYLDAY SLLQAAKVNK NWNELASSDV LWRKLCQKRW LYCDRVTLQL HGLETWKQFF ISRTWQEHAK TRAKPEDFN YKEIPVAFEF RAHPCYISRH GLIRNGQGKS AVCMVTSTNR ISTWDVHEGA MTWVSPVQPS YITRMTTLPE M HIAVTIDM QSNIKLWDCH NRKVLATTGL LSSCQLLQAV FTNDSPIVLV GDILGNLYIF RIPDLHLISK VNVFPYGIDE LH CSPQKKW VLLIGKQRHV LTKVFYMSSL LRTSEFSAPV STDLKFSLCQ RAFWTPRRED RITLMSSTIP PDPTKFATFD MKL EEIENK VTIQGHLVAS FSLQDCKERA EWMGVSDKDV IVCSTGSSLL LFDINGLRLQ TFQYCPEEIL RLCVDPVHVI VTCN NGSLD VYVWEERSPL LRRCYRLRKR GYLPLSGFII KTLCDESSII LVMTSSPIPC FLMAYTLKVC S

UniProtKB: F-box domain-containing protein

Macromolecule #14: S-phase kinase-associated protein 1

• Macromolecule: Name: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 14 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 18.693992 KDa

Sequence

String:

MPTIKLQSSD GEIFEVDVEI AKQSVTIKTM LEDLGMDDEG DDDPVPLPNV NAAILKKVIQ WCTHHKDDPP PPEDDENKEK RTDDIPVWD QEFLKVDQGT LFELILAANY LDIKGLLDVT CKTVANMIKG KTPEEIRKTF NIKNDFTEEE EAQVRKENQW C EEK

UniProtKB: S-phase kinase-associated protein 1

Macromolecule #15: Expressed sequence C85627

• Macromolecule: Name: Expressed sequence C85627 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 54.205703 KDa

Sequence

String:

METHLPSLPS LPMMKILSYL DAYSLLQVAQ VNKNWNALAS SDVLWRKLCQ KRWLYCDTVI LQLHDKETWK QFFVNRTYQE HTKTRAKPE DFTYKEICAE TGIWAYACYI SGRGLTRNGQ GTSVVCMLTS MTKISTWDIH EGVMTWVSPV QPTTIKLLNT L PEMHIAVT VDIHSTIKLW DCNSSDALAT NNLFFPCQTL KSVFTKDAAI VLVSDTLGNL YIFRIPDLHL ISTINVFPYG IN ELYCSPQ KKWVFLSRKH PHILPKVFYM NSLLRRSEFS APVSTVLNFS LCDKAFWTPR KEDRITLMSI SAPYKVTKFV TFD MKLEEI GNQIIVTGYL IASFSLTDYE GRLECFGVSD KDVIVCSTGS SLLLFSIYGV CLQTFDYCSE EILRLWVDPF HVIV TFIDG SLDVYAWEER CQQLSKCYRL QNRRRLPRQS CFEKTLCDEV SIIRMVRNGR NPCYLMTYTL NIHS

UniProtKB: Expressed sequence C85627

Macromolecule #16: F-box and WD-40 domain protein 21

• Macromolecule: Name: F-box and WD-40 domain protein 21 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 54.517043 KDa

Sequence

String:

MEIHLPRLPL MEIFSYLDAY SLLQVAQVNK NWNELASSDV LWRKLCQKRW FYCNMVTQQL LGKETWKEFF IYRTWQEHAK SRAKPEDFI YKEIPAEYGI QAYACYISEH GLTRNGQGRS VICMATSMNR ISTWDIHEGV LTWVSPEQPA SIKLLTTLPE M YIAVTVDM ESTIKLWDCH NSEALATNSL ISPCQSLKAV ITKDGPIVLI GDTLGNLNIF RIPDLYHITR LKVFPYGISE LY CSPQKKW IFLNRKHPHI LPKVFYMSSL LRTSEFSAPV STDLKFSLCQ RAFWTPRRED RITLMSIHGP KKIKKFITFD MEL EKIGNK ITVKEHFFAS FSLQNYEERP EWYGVSDKDV IVCSTRFSLL LFDINGHCLQ AFQYCPEQIL RLWVDPLHVI VSCN DGFLD VYAWEERSQQ LNKCYRLQYS KHLPSSGLIN KTLSDDVSII QVITIRTTPC FLMAFILKSA LEN

UniProtKB: F-box domain-containing protein

Macromolecule #17: GUANOSINE-5'-TRIPHOSPHATE

• Macromolecule: Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 2 / Formula: GTP
• Molecular weight: Theoretical: 523.18 Da

Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

Macromolecule #18: MAGNESIUM ION

• Macromolecule: Name: MAGNESIUM ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: MG
• Molecular weight: Theoretical: 24.305 Da

Macromolecule #19: ZINC ION

• Macromolecule: Name: ZINC ION / type: ligand / ID: 19 / Number of copies: 11 / Formula: ZN
• Molecular weight: Theoretical: 65.409 Da

Macromolecule #20: CALCIUM ION

• Macromolecule: Name: CALCIUM ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: CA
• Molecular weight: Theoretical: 40.078 Da

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.4
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.8 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: NONE
• Final reconstruction: Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 249541
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION