EMDB-55607: Cytoplasmic lattice filament repeat unit with ubiquitin

Basic information

Entry

Database: EMDB / ID: EMD-55607

• Title: Cytoplasmic lattice filament repeat unit with ubiquitin

Sample

• Complex: Multi-subunit complex of cytoplasmic lattice repeat unit with bound ubiquitin
  • Protein or peptide: x 15 types

• Keywords: Ubiquitination / Complex / Filament / UNKNOWN FUNCTION

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 / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Chromatin modifying enzymes / ER Quality Control Compartment (ERQC) / protein storage / structural constituent of cytoplasmic lattice / cytoplasmic lattice / Regulation of PTEN localization / cortical granule exocytosis / Downregulation of ERBB2:ERBB3 signaling / establishment or maintenance of apical/basal cell polarity / IRAK2 mediated activation of TAK1 complex / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / endoplasmic reticulum localization / Gap-filling DNA repair synthesis and ligation in GG-NER / Fanconi Anemia Pathway / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of expression of SLITs and ROBOs / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Downregulation of ERBB4 signaling / Stabilization of p53 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Alpha-protein kinase 1 signaling pathway / Regulation of pyruvate metabolism / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / PD-L1(CD274) glycosylation and translocation to plasma membrane / Translesion synthesis by REV1 / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Translesion synthesis by POLK / Pexophagy / Regulation of NF-kappa B signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Regulation of TP53 Activity through Methylation / Carboxyterminal post-translational modifications of tubulin / Intraflagellar transport / Translesion synthesis by POLI / Recognition of DNA damage by PCNA-containing replication complex / NRIF signals cell death from the nucleus / Interferon alpha/beta signaling / p75NTR recruits signalling complexes / Negative regulation of MAPK pathway / Spry regulation of FGF signaling / Regulation of TP53 Degradation / Translesion Synthesis by POLH / Activated NOTCH1 Transmits Signal to the Nucleus / Formation of TC-NER Pre-Incision Complex / Negative regulation of MET activity / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Termination of translesion DNA synthesis / COPI-independent Golgi-to-ER retrograde traffic / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Senescence-Associated Secretory Phenotype (SASP) / Josephin domain DUBs / DNA Damage Recognition in GG-NER / Dual Incision in GG-NER / Ubiquitin-dependent degradation of Cyclin D / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / Downregulation of ERBB2 signaling / Dual incision in TC-NER / E3 ubiquitin ligases ubiquitinate target proteins / Oncogene Induced Senescence / Degradation of CRY and PER proteins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TNFR1-induced NF-kappa-B signaling pathway / HDR through Homologous Recombination (HRR) / Gap-filling DNA repair synthesis and ligation in TC-NER / Metalloprotease DUBs / Formation of Incision Complex in GG-NER / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / mRNA Polyadenylation / EGFR downregulation / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA

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. / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / DAPIN domain / PAAD/DAPIN/Pyrin domain / PAAD/DAPIN/Pyrin domain / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation 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 / Ring finger / Tubulin/FtsZ family, GTPase domain / 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 domain signature. / Ubiquitin conserved site / Ubiquitin domain / 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.

Component:

NLR family, pyrin domain containing 4F / Polyubiquitin-C / Ubiquitin-conjugating enzyme E2 D3 / Tubulin beta-4B chain / Tubulin alpha-1C chain / 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 / S-phase kinase-associated protein 1 / Transducin-like enhancer protein 6

• Biological species: Mus musculus (house mouse)
• Method: subtomogram averaging / cryo EM / Resolution: 7.7 Å
• Authors: Singh K / Harasimov K / Carter A

Funding support

United Kingdom, European Union, 3 items

Organization	Grant number	Country
Medical Research Council (MRC, United Kingdom)	MC_UP_A025_1011	United Kingdom
European Molecular Biology Organization (EMBO)	ALTF 426-2023	European Union
Wellcome Trust	221856/Z/20/Z	United Kingdom

• Citation: Journal: EMBO J / Year: 2026; Title: In-situ cryo-ET of mouse embryos reveals cytoplasmic lattices contain ubiquitin-charged E2-E3 ligase assemblies.; Authors: Kashish Singh / Katarina Harasimov / Kathy K Niakan / Andrew P Carter / ; Abstract: Cytoplasmic lattices (CPLs) are filamentous assemblies essential for mammalian embryonic development. They are known to regulate organelle organization, spindle assembly, and protein homeostasis, but their molecular functions remain unclear. Here, we develop a strategy combining cryo-focused ion beam milling and cryo-electron tomography to resolve macromolecular complexes directly in mammalian embryos. Using this approach, we determine the in situ structure of cytoplasmic lattices within 6/8-cell mouse embryos at ~4.7 Å resolution. CPL filaments are built from multiple copies of at least fourteen proteins arranged into a ~4.5 MDa repeating unit. The repeat contains a central cavity that is open at the back and lined with multiple FBXW-SKP1 complexes and three modules, each containing the E2 ubiquitin-conjugating enzyme UBE2D and the E3 ligase UHRF1. We resolve two CPL states: one is consistent with a ubiquitin-charged UBE2D, where ubiquitin is held in an open, inactive conformation by binding the scaffold protein PADI6; the second lacks discernible ubiquitin density and shows structural changes compatible with ubiquitin becoming available for transfer. Our findings support a model in which CPLs function as large ubiquitin ligase assemblies during early embryonic development.

History

Deposition	Nov 6, 2025	-
Header (metadata) release	Aug 12, 2026	-
Map release	Aug 12, 2026	-
Update	Aug 26, 2026	-
Current status	Aug 26, 2026	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_55607.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 2.37 Å

Density

Contour Level	By AUTHOR: 0.056
Minimum - Maximum	-0.114346586 - 0.22693123
Average (Standard dev.)	-0.000000000000125 (±0.014978175)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 256 256 256 Spacing 256 256 256
Cell	A=B=C: 606.72 Å α=β=γ: 90.0 °

Supplemental data

Mask #1

• File: emd_55607_msk_1.map

Additional map: Unsharpened map

• File: emd_55607_additional_1.map
• Annotation: Unsharpened map

Additional map: Map after focussed 3D refinement only on the...

• File: emd_55607_additional_2.map
• Annotation: Map after focussed 3D refinement only on the asymmetric part of the repeat unit

Half map: #2

• File: emd_55607_half_map_1.map

Half map: #1

• File: emd_55607_half_map_2.map

Sample components

Entire : Multi-subunit complex of cytoplasmic lattice repeat unit with bou...

• Entire: Name: Multi-subunit complex of cytoplasmic lattice repeat unit with bound ubiquitin

Components

• Complex: Multi-subunit complex of cytoplasmic lattice repeat unit with bound ubiquitin
  • Protein or peptide: KH domain-containing protein 3
  • Protein or peptide: Inactive protein-arginine deiminase type-6
  • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
  • Protein or peptide: Transducin-like enhancer protein 6
  • Protein or peptide: Oocyte-expressed protein homolog
  • Protein or peptide: Zinc finger BED domain-containing protein 3
  • Protein or peptide: NLR family, pyrin domain containing 4F
  • 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: Tubulin alpha-1C chain
  • Protein or peptide: Tubulin beta-4B chain
  • Protein or peptide: F-box/WD repeat-containing protein
  • Protein or peptide: S-phase kinase-associated protein 1
  • Protein or peptide: Polyubiquitin-C

Supramolecule #1: Multi-subunit complex of cytoplasmic lattice repeat unit with bou...

• Supramolecule: Name: Multi-subunit complex of cytoplasmic lattice repeat unit with bound ubiquitin; type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
• Source (natural): Organism: Mus musculus (house mouse)

Macromolecule #1: KH domain-containing protein 3

• Macromolecule: Name: KH domain-containing protein 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / 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 #2: Inactive protein-arginine deiminase type-6

• Macromolecule: Name: Inactive protein-arginine deiminase type-6 / type: protein_or_peptide / ID: 2 / Number of copies: 24 / 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 #3: NACHT, LRR and PYD domains-containing protein 5

• Macromolecule: Name: NACHT, LRR and PYD domains-containing protein 5 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / 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 #4: Transducin-like enhancer protein 6

• Macromolecule: Name: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / 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: Oocyte-expressed protein homolog

• Macromolecule: Name: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 5 / Number of copies: 4 / 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 #6: Zinc finger BED domain-containing protein 3

• Macromolecule: Name: Zinc finger BED domain-containing protein 3 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / 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

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: 4 / 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: NACHT, LRR and PYD domains-containing protein 14

• Macromolecule: Name: NACHT, LRR and PYD domains-containing protein 14 / type: protein_or_peptide / ID: 8 / Number of copies: 3 / 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 #9: E3 ubiquitin-protein ligase UHRF1

• Macromolecule: Name: E3 ubiquitin-protein ligase UHRF1 / type: protein_or_peptide / ID: 9 / Number of copies: 3 / 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 #10: Ubiquitin-conjugating enzyme E2 D3

• Macromolecule: Name: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 10 / Number of copies: 3 / 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 #11: Tubulin alpha-1C chain

• Macromolecule: Name: Tubulin alpha-1C chain / type: protein_or_peptide / ID: 11 / Number of copies: 3 / 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 #12: Tubulin beta-4B chain

• Macromolecule: Name: Tubulin beta-4B chain / type: protein_or_peptide / ID: 12 / Number of copies: 3 / 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 #13: F-box/WD repeat-containing protein

• Macromolecule: Name: F-box/WD repeat-containing protein / type: protein_or_peptide / ID: 13 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 39.676895 KDa

Sequence

String:

(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)

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: 4 / 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: Polyubiquitin-C

• Macromolecule: Name: Polyubiquitin-C / type: protein_or_peptide / ID: 15 / Number of copies: 3 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 8.576831 KDa

Sequence

String:

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-C

Experimental details

Structure determination

• Method: cryo EM
• Processing: subtomogram averaging
• Aggregation state: filament

Sample preparation

• Buffer: pH: 7.5
• Vitrification: Cryogen name: ETHANE

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 3.5 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: 4.0 µm / Nominal defocus min: 1.0 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.1) / Number subtomograms used: 30490
• Extraction: Number tomograms: 1153 / Number images used: 134387 / Software - Name: RELION (ver. 5.1)
• CTF correction: Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Final angle assignment: Type: MAXIMUM LIKELIHOOD