EMDB-65575: Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte

Basic information

Entry

Database: EMDB / ID: EMD-65575

• Title: Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte

Sample

• Complex: mouse oocyte cytoplasmic lattices (CPL)
  • Protein or peptide: x 14 types
• Ligand: x 2 types

• Keywords: Cytoplasmic lattice / Maternal complex / Cryo-EM structure / Protein assembly / STRUCTURAL PROTEIN

Function / homology

Function:

ooplasm / regulation of translation by machinery localization / Prolactin receptor signaling / Signaling by BMP / 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 / embryonic process involved in female pregnancy / 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 / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / SCF-beta-TrCP mediated degradation of Emi1 / COPI-independent Golgi-to-ER retrograde traffic / E3 ubiquitin ligases ubiquitinate target proteins / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Downregulation of SMAD2/3:SMAD4 transcriptional activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cytoplasm organization / Regulation of BACH1 activity / histone H3K18 ubiquitin ligase activity / histone H3K14 ubiquitin ligase activity / histone H3 ubiquitin ligase activity / PINK1-PRKN Mediated Mitophagy / Inactivation of CSF3 (G-CSF) signaling / SCF(Skp2)-mediated degradation of p27/p21 / histone H3K23 ubiquitin ligase activity / spermatogonial cell division / MAP3K8 (TPL2)-dependent MAPK1/3 activation / COPI-mediated anterograde transport / Regulation of TNFR1 signaling / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Kinesins / histone H3 reader activity / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / Cyclin D associated events in G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / cortical granule / Orc1 removal from chromatin / IKK complex recruitment mediated by RIP1 / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / PKR-mediated signaling / Aggrephagy / RHO GTPases activate IQGAPs / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of establishment of protein localization / Resolution of Sister Chromatid Cohesion / Degradation of beta-catenin by the destruction complex / Activation of NF-kappaB in B cells / Recycling pathway of L1 / Iron uptake and transport / The role of GTSE1 in G2/M progression after G2 checkpoint / positive regulation of embryonic development / apical cortex / chromosomal DNA methylation maintenance following DNA replication / intermediate filament cytoskeleton / positive regulation of meiotic nuclear division / regulation of RNA stability / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Hedgehog 'off' state / Interleukin-1 signaling / RHO GTPases Activate Formins / F-box domain binding / Separation of Sister Chromatids / Downstream TCR signaling / Recruitment of NuMA to mitotic centrosomes / hemi-methylated DNA-binding / Peroxisomal protein import / GLI3 is processed to GLI3R by the proteasome / Regulation of PLK1 Activity at G2/M Transition / embryonic pattern specification / regulation of epithelial cell proliferation / Neddylation / PcG protein complex / embryonic cleavage / MHC class II antigen presentation / fertilization / mitochondrion localization / gap junction / establishment of spindle localization / (E3-independent) E2 ubiquitin-conjugating enzyme / embryonic brain development / maintenance of protein location in nucleus / positive regulation of epithelial cell apoptotic process / Cul7-RING ubiquitin ligase complex

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 / 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 / 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 / SKP1/BTB/POZ 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

Component:

NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 / Oocyte-expressed protein homolog / Tubulin beta-2B chain / 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: 4.2 Å
• Authors: Liu SX / Xue JC / Zhang Y / Liu YS / Gao HS / Shen EZ

Funding support

China, 2 items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	32070628	China
National Natural Science Foundation of China (NSFC)	32271258	China

• Citation: Journal: Nature / Year: 2026; Title: Molecular basis of oocyte cytoplasmic lattice assembly.; Authors: Shuxian Liu / Yusong Liu / Junchao Xue / Zhenzhen Li / Yan Zhang / Bailun Li / Lidan Xu / Lili Li / Zhenzhen Yu / Hongtao Yu / Haishan Gao / En-Zhi Shen / ; Abstract: Mammalian oocytes are filled with fibric structures called cytoplasmic lattice (CPL) that are essential for oocyte maturation and early embryonic development. CPL comprises subcortical maternal complex (SCMC) and multiple components, including PADI6. Although it was first discovered in the 1960s, the molecular architecture and assembly mechanisms of CPL remain poorly understood. Here we present the cryo-electron microscopy structure of CPL isolated from mouse oocytes. Our analysis identified 14 constitutive protein subunits and revealed that CPL is composed of repeating units comprising U-shaped basket (UB) and adapter ring (AR) features, forming a filamentous architecture. The AR adopts a two-fold symmetric conformation, containing two NLRP4F, four SCMC and two ZBED3 subunits circularized via two distinct interaction clusters. The UB is anchored by PADI6, a didecamer composed of ten homodimers assembled by two back-to-back pentamers, each forming the lateral side of the UB. The underfoot base and up and down sides of the UB are formed by multiple central-symmetric assemblies (UBE2D3-UHRF1-NLRP14) and (TUBB2B-TUBB2A-FBXW24-SKP1), respectively, associating with the PADI6 pentamers to construct the intact UB structure. Two SCMC dimers within each AR connect the up and down sides of two adjacent UBs with an extensive protein-protein interaction network, and thus maintain the repetitive connection between the neighbouring CPL units. Our work unveils the architectural principles underlying the assembly of this large, periodic CPL filament, offering a molecular basis for understanding the functions of CPL in early mammalian embryogenesis and female reproductive disorders.

History

Deposition	Jul 28, 2025	-
Header (metadata) release	Feb 25, 2026	-
Map release	Feb 25, 2026	-
Update	Jun 24, 2026	-
Current status	Jun 24, 2026	Processing site: PDBc / Status: Released

Map

• File: Download / File: emd_65575.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.0773 Å

Density

Contour Level	By AUTHOR: 0.085
Minimum - Maximum	-0.50288993 - 1.0568854
Average (Standard dev.)	-0.0010518647 (±0.024199657)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 640 640 640 Spacing 640 640 640
Cell	A=B=C: 689.472 Å α=β=γ: 90.0 °

Supplemental data

Half map: #2

• File: emd_65575_half_map_1.map

Half map: #1

• File: emd_65575_half_map_2.map

Sample components

Entire : mouse oocyte cytoplasmic lattices (CPL)

• Entire: Name: mouse oocyte cytoplasmic lattices (CPL)

Components

• Complex: mouse oocyte cytoplasmic lattices (CPL)
  • Protein or peptide: Inactive protein-arginine deiminase type-6
  • Protein or peptide: Oocyte-expressed protein homolog
  • Protein or peptide: KH domain-containing protein 3
  • Protein or peptide: NLR family, pyrin domain containing 4F
  • Protein or peptide: FBXW24
  • Protein or peptide: S-phase kinase-associated protein 1
  • 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
  • Protein or peptide: NACHT, LRR and PYD domains-containing protein 14
  • Protein or peptide: Tubulin beta-2A chain
  • Protein or peptide: Tubulin beta-2B chain
  • Protein or peptide: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5
  • Protein or peptide: Transducin-like enhancer protein 6
• Ligand: GUANOSINE-5'-DIPHOSPHATE
• Ligand: ADENOSINE-5'-DIPHOSPHATE

Supramolecule #1: mouse oocyte cytoplasmic lattices (CPL)

• Supramolecule: Name: mouse oocyte cytoplasmic lattices (CPL) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#14
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 2 MDa

Macromolecule #1: Inactive protein-arginine deiminase type-6

• Macromolecule: Name: Inactive protein-arginine deiminase type-6 / type: protein_or_peptide / ID: 1 / Number of copies: 20 / 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 #2: Oocyte-expressed protein homolog

• Macromolecule: Name: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 14.294582 KDa

Sequence

String:

NVLPVSLRLR TRPWWFPIQE VSNPLVLYME AWVAERVIGT DQAEISEIEW MCQALLTVDS VNSGNLAEIT IFGQPSAQTR MKNILLNMA AWHKENELQR AVKVKEVEEF LKIRASSILS KLSKKG

UniProtKB: Oocyte-expressed protein homolog

Macromolecule #3: KH domain-containing protein 3

• Macromolecule: Name: KH domain-containing protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 15.250954 KDa

Sequence

String:

MASLKRFQTL VPLDHKQGTL FEIIGEPKLP KWFHVECLED PKRLYVEPRL LEIMFGKDGE HIPHLESMLH TLIHVNVWGP ERRAEIWIF GPPPFRRDVD RMLTDLAHYC RMKLMEIEAL EAGVERRRM

UniProtKB: KH domain-containing protein 3

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

• Macromolecule: Name: NLR family, pyrin domain containing 4F / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 107.564766 KDa

Sequence

String:

ISDFGLIWYL RELNKKEFMK FKDFLIQEIL ELKLKQVSST KVKKASREDL ANLLLKCGEN QAWDMTFRIL QKINRKDLTE RATGAIVGN PNLYRDHLKK KLTHDCPKKF NVRIQDFIKE TFIQNDYDAF ENLLISKGTE RKPHMVFLKG MAGVGKTLML K NLMLAWSK GLVFQNKFSY AFYFCCQDVK QLKTASLAEL ISREWPSPSA PIEEILSQPE KLLFIIDSLE GMEWDLTKQE SE LCDDCME KQPVSTLLSS LLRRKMLPES SLLLSTTPET FEKMEDRIQC TDVKTATAFD ERSMKIYFHR LFQDRKRAQE AFS LVRENK QLFTICQVPL LCWMVATCLK EEIEKGGDPV SLCRRTTSLY TTHIFSLFIP QSAQYPSKKS QDQLQGLCSL AAEG MWTDT FVFGKEALRR NGIFDSDIPT LLDIGMLGKI REFENSYIFL HPSVQEVCAA IFYMLKRHVE HPSQDVKNIE TVLFM FLKK VKTQWIFLGC FIFGLLQKSE QEKLGVFFGH RLSKNIHHKL YQCLETLSGN AELQEQIDGM RLFSCLFEME DEAFLV KAM NCMQQINFVA KNYSDFIVAA YCLKHCSTLK KLSFSTENVL NEGDQSYMEE LLICWNNMCS VFVRSKDIQE LRIKDTN FN EPAIRVLYES LKYPSFTLNK LVANNVSFGD NHVLFELIQN SSLQYLDLSC SFLSHNEVKL LCDILNQAEC NIEKLMIA H CKLSPDDCKI FGSILMSSKS LKVLNLASNN LNQGISSLCK ALCHPHCTLE YLVLSNCSLS EQCWDYLSEV LRQNKTLSH LDISSNDLKD EGLKILCRSL ILPYCVLESL CLSCCGITER GCQDLAEVLK NNQNLKYLHV SYNKLKDTGV MLLCDAIKHP NCHLKDLQL EACEITDASN EELCYAFMQC ETLQTLNLMG NAFEVSRMVF FPRF

UniProtKB: NLR family, pyrin domain containing 4F

Macromolecule #5: FBXW24

• Macromolecule: Name: FBXW24 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 53.469059 KDa

Sequence

String:

MEIHLSSFPM MEIFSYLDAY SLLQVAQVNK NWNALASNDF LWRKLCQERW LFCDMVTLQL LGKETWKQFF VYRTWQEHVK SRAIPEDFT YKEIPLECGV RGYAGYISGC ALTRNGQGKS VVCMVSSKNK ISTWDISESV ITWVSPVQPA SIKLLTTLPD M HIAVTVDI QSTIKLWDCH NREALATNNL ESPCKSLKAV ISKDGPIVLA GDILGNLYIF RIPDLHLIST VNVFPCGFDK ID CSPQKKW VLLSQNHPCI YPKVFYMSSL LRTSEFSDPV STVLEFSLCK RAFWTPRRED RITLMSRRGR PIVTRFETFD MKL EENGNK TIVKGDLVAS FSLQDYNENP KWMGVSDKSV IVCSTGSSLL LFSMKGLHLQ TFQYSPEMIV RLWVDPVHVI ITCN DGSID VYMWEERSLL LKMCYRLQNG RHLPPFGFIK NLLCDDVSIV QLMIDRQGPC FLMAYTLNIC S

Macromolecule #6: S-phase kinase-associated protein 1

• Macromolecule: Name: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / 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 #7: Ubiquitin-conjugating enzyme E2 D3

• Macromolecule: Name: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 7 / 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 #8: E3 ubiquitin-protein ligase UHRF1

• Macromolecule: Name: E3 ubiquitin-protein ligase UHRF1 / type: protein_or_peptide / ID: 8 / Number of copies: 4 / 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 #9: Zinc finger BED domain-containing protein 3

• Macromolecule: Name: Zinc finger BED domain-containing protein 3 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 6.370292 KDa

Sequence

String:

SYSEAWGYFH LDPAQPRHRM MSAWATCRLC GLQVGGLPNF QMWTRALCQH LSDVH

UniProtKB: Zinc finger BED domain-containing protein 3

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: 110.368961 KDa

Sequence

String:

IDYRTVIKEN IFTMWYKTSL HGEFATLNCV ITPKDQNLLQ HIFDEDIQTS EAPQTVVLQG AAGIGKTTLL KKAVLEWADG NLYQQFTHV FYLNGKEISQ VKEKSFAQLI SKHWPSSEGP IEQVLSKPSS LLFIIDSFDE LDFSFEEPQF ALCKDWTQIS P VSFLISSL LRKVMLPESY LLVATRSTAW KRLVPLLQKP QRVKLSGLSK NARMDYIHHL LKDKAWATSA IYSLRMNWRL FH MCHVCHM CQMICAVLKG QVEKGGRVEE TCKTSTALFT YYICSLFPRI PVGCVTLPNE TLLRSLCKAA VEGIWTMKHV LYQ QNLRKH ELTREDILLF LDAKVLQQDT EYENCYMFTH LHVQEFFAAL FYLLRENLEE QDYPSEPFEN LYLLLESNHI HDPH LEQMK CFLFGLLNKD RVRQLEETFN LTISMEVREE LLACLEGLEK DDSSLSQLRF QDLLHCIYET QDQEFITQAL MYFQK IIVR VDEEPQLRIY SFCLKHCHTL KTMRLTARAD LKNMLDTAEM CLEGAAVQVI HYWQDLFSVL HTNESLIEMD LYESRL DES LMKILNEELS HPKCKLQKLI FRAVDFLNGC QDFTFLASNK KVTHLDLKET DLGVNGLKTL CEALKCKGCK LRVLRLA SC DLNVARCQKL SNALQTNRSL VFLNLSLNNL SNDGVKSLCE VLENPNSSLE RLALASCGLT KAGCKVLSSA LTKSKRLT H LCLSDNVLED EGIKLLSHTL KHPQCTLQSL VLRSCSFTPI GSEHLSTALL HNRSLVHLDL GQNKLADNGV KLLCHSLQQ PHCNLQELEL MSCVLTSKAC GDLASVLVNN SNLWSLDLGH NILDDAGLNI LCDALRNPNC HVQRLGLENC GLTPGCCQDL LGILSNNKS VIQMNLMKNA LDHESIKNLC KVLRSPTCKM EFLALDKKEI LKKKIKKFLV DVRINNPHLV IGPECPNTES G CWWNYF

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

Macromolecule #11: Tubulin beta-2A chain

• Macromolecule: Name: Tubulin beta-2A chain / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 49.953797 KDa

Sequence

String:

MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYSIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta-2A chain

Macromolecule #12: Tubulin beta-2B chain

• Macromolecule: Name: Tubulin beta-2B chain / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 49.999887 KDa

Sequence

String:

MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta-2B chain

Macromolecule #13: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5

• Macromolecule: Name: Isoform 4 of NACHT, LRR and PYD domains-containing protein 5; type: protein_or_peptide / ID: 13 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 109.296773 KDa

Sequence

String:

DLQDYKAHVI AKFDTSVDLH YDSPEMKLLS DAFKPYQKTF QPHTIILHGR PGVGKSALAR SIVLGWAQGK LFQKMSFVIF FSVREIKWT EKSSLAQLIA KECPDSWDLV TKIMSQPERL LFVIDGLDDM DSVLQHDDMT LSRDWKDEQP IYILMYSLLR K ALLPQSFL IITTRNTGLE KLKSMVVSPL YILVEGLSAS RRSQLVLENI SNESDRIQVF HSLIENHQLF DQCQAPSVCS LV CEALQLQ KKLGKRCTLP CQTLTGLYAT LVFHQLTLKR PSQSALSQEE QITLVGLCMM AAEGVWTMRS VFYDDDLKNY SLK ESEILA LFHMNILLQV GHNSEQCYVF SHLSLQDFFA ALYYVLEGLE EWNQHFCFIE NQRSIMEVKR TDDTRLLGMK RFLF GLMNK DILKTLEVLF EYPVIPTVEQ KLQHWVSLIA QQVNGTSPMD TLDAFYCLFE SQDEEFVGGA LKRFQEVWLL INQKM DLKV SSYCLKHCQN LKAIRVDIRD LLSVDNTLEL CPVVTVQETQ CKPLLMEWWG NFCSVLGSLR NLKELDLGDS ILSQRA MKI LCLELRNQSC RIQKLTFKSA EVVSGLKHLW KLLFSNQNLK YLNLGNTPMK DDDMKLACEA LKHPKCSVET LRLDSCE LT IIGYEMISTL LISTTRLKCL SLAKNRVGVK SMISLGNALS SSMCLLQKLI LDNCGLTPAS CHLLVSALFS NQNLTHLC L SNNSLGTEGV QQLCQFLRNP ECALQRLILN HCNIVDDAYG FLAMRLANNT KLTHLSLTMN PVGDGAMKLL CEALKEPTC YLQELELVDC QLTQNCCEDL ACMITTTKHL KSLDLGNNAL GDKGVITLCE GLKQSSSSLR RLGLGACKLT SNCCEALSLA ISCNPHLNS LNLVKNDFST SGMLKLCSAF QCPVSNLGII GLWKQEYYAR VRRQLEEVEF VKPHVVIDGD WYASDEDDRN W WKN

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

Macromolecule #14: Transducin-like enhancer protein 6

• Macromolecule: Name: Transducin-like enhancer protein 6 / type: protein_or_peptide / ID: 14 / Number of copies: 4 / Enantiomer: LEVO
• Source (natural): Organism: Mus musculus (house mouse)
• Molecular weight: Theoretical: 49.00534 KDa

Sequence

String:

DPQPVWDAEP QFCQGFLIQG LWELFMDSRQ KNQQEHGGED SSQESKDSGL CDFKPEPQPR HRNSLSDSAD PFLIKSPSAL LDYYQEDVS RPQPETQESS GRADKFLKPL SWGSEVLESS CNQPSTALWQ LERFTVPQAL QKVRVLKHQE LLLVVAVSSF T RHVFTCSQ SGIKVWNLVN QVAEDRDPES HLKCSVQDNK VYLRTCLLSS NSRTLFAGGY NLPGVIVWDL AAPSLYEKCQ LP CEGLSCQ ALANTKENMA LAGFTDGTVR IWDLRTQEIV RNLKGPTNSA RNLVVKDDNI WTGGLDACLR CWDLRMAKVS LEH LFQSQI MSLAHSPTED WLLLGLANGQ HCLFNSRKRD QVLTVDTKDN TILGLKFSPN GKWWASVGMG NFITVHSMPT GAKL FQVPE VGPVRCFDMT ENGRLIITGS RDCASVYHIK Y

UniProtKB: Transducin-like enhancer protein 6

Macromolecule #15: GUANOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 15 / Number of copies: 4 / Formula: GDP
• Molecular weight: Theoretical: 443.201 Da

Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

Macromolecule #16: ADENOSINE-5'-DIPHOSPHATE

• Macromolecule: Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 16 / Number of copies: 4 / Formula: ADP
• Molecular weight: Theoretical: 427.201 Da

Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

Experimental details

Structure determination

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

Sample preparation

• Buffer: pH: 7.5
• Grid: Model: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: TFS KRIOS
• Image recording: Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• CTF correction: Type: NONE

Startup model

Type of model: EMDB MAP
EMDB ID:

34556

• 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: cryoSPARC / Number images used: 676923
• Initial angle assignment: Type: ANGULAR RECONSTITUTION
• Final angle assignment: Type: ANGULAR RECONSTITUTION