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- EMDB-69647: Structure of oocyte cytoplasmic lattices -

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Basic information

Entry
Database: EMDB / ID: EMD-69647
TitleStructure of oocyte cytoplasmic lattices
Map data
Sample
  • Complex: Structure of oocyte cytoplasmic lattices
    • Protein or peptide: x 16 types
  • Ligand: x 4 types
Keywordsoocytes cytoplasmic lattices / CELL CYCLE
Function / homology
Function and homology information


regulation of translation by machinery localization / ooplasm / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / establishment of organelle localization / Cargo trafficking to the periciliary membrane / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Sealing of the nuclear envelope (NE) by ESCRT-III / Chromatin modifying enzymes ...regulation of translation by machinery localization / ooplasm / Prolactin receptor signaling / Signaling by BMP / subcortical maternal complex / establishment of organelle localization / Cargo trafficking to the periciliary membrane / Microtubule-dependent trafficking of connexons from Golgi to the plasma 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 / embryonic process involved in female pregnancy / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / endoplasmic reticulum localization / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / establishment or maintenance of apical/basal cell polarity / SCF-beta-TrCP mediated degradation of Emi1 / COPI-independent Golgi-to-ER retrograde traffic / E3 ubiquitin ligases ubiquitinate target proteins / 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 / 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 / positive regulation of meiotic nuclear division / regulation of RNA stability / intermediate filament cytoskeleton / 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 / Neddylation / regulation of epithelial cell proliferation / PcG protein complex / embryonic pattern specification / embryonic cleavage / MHC class II antigen presentation / mitochondrion localization / gap junction / establishment of spindle localization / (E3-independent) E2 ubiquitin-conjugating enzyme / maintenance of protein location in nucleus / fertilization / Cul7-RING ubiquitin ligase complex / Antigen processing: Ubiquitination & Proteasome degradation / methyl-CpG binding
Similarity search - Function
Zinc finger BED domain-containing protein 2/3 / : / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 ...Zinc finger BED domain-containing protein 2/3 / : / BED zinc finger / KH-like RNA-binding domain / : / KH-like RNA-binding domain / Groucho/transducin-like enhancer / : / UHRF1, tandem tudor domain / Tandem tudor domain within UHRF1 / UHRF1/2-like / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / SRA-YDG / SRA-YDG superfamily / SAD/SRA domain / YDG domain profile. / SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. / : / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / A Receptor for Ubiquitination Targets / NOD2, winged helix domain / NOD2 winged helix domain / F-box domain profile. / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / F-box-like / DAPIN domain / PAAD/DAPIN/Pyrin domain / F-box-like domain superfamily / 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 / 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
Similarity search - Domain/homology
NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / F-box domain-containing protein / F-box domain-containing protein / Inactive protein-arginine deiminase type-6 / E3 ubiquitin-protein ligase UHRF1 ...NLR family, pyrin domain containing 4F / Ubiquitin-conjugating enzyme E2 D3 / Tubulin alpha-1C chain / Expressed sequence C85627 / NACHT, LRR and PYD domains-containing protein 14 / Tubulin beta-2A chain / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLiu Q / Gui M
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Vita / Year: 2026
Title: Hierarchical assembly of native cytoplasmic lattices revealed by cryo-EM
Authors: Zhang YL / Liu Y / Liu Q / Zhang Q / Jin J / Liu S / Yang S / Liu Y / Peng YJ / Lai M / Sun Y / Zhang YY / Mei Y / Tong X / Zhang S / Gui M
History
DepositionMar 10, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69647.png

Downloads & links

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Map

FileDownload / File: emd_69647.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å		0.93 Å/pix.
x 400 pix.
= 372. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum0.0 - 0.040565364
Average (Standard dev.)0.00023133849 (±0.0011301232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 372.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Structure of oocyte cytoplasmic lattices

EntireName: Structure of oocyte cytoplasmic lattices
Components
  • Complex: Structure of oocyte cytoplasmic lattices
    • Protein or peptide: F-box and WD-40 domain protein 19
    • Protein or peptide: F-box and WD-40 domain protein 21
    • Protein or peptide: Inactive protein-arginine deiminase type-6
    • Protein or peptide: NLR family, pyrin domain containing 4F
    • Protein or peptide: Oocyte-expressed protein homolog
    • Protein or peptide: Isoform 2 of KH domain-containing protein 3
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 5
    • Protein or peptide: Transducin-like enhancer protein 6
    • Protein or peptide: Zinc finger BED domain-containing protein 3
    • Protein or peptide: Tubulin beta-2A chain
    • Protein or peptide: Tubulin alpha-1C chain
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
    • Protein or peptide: E3 ubiquitin-protein ligase UHRF1
    • Protein or peptide: NACHT, LRR and PYD domains-containing protein 14
    • Protein or peptide: S-phase kinase-associated protein 1
    • Protein or peptide: Expressed sequence C85627
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: Structure of oocyte cytoplasmic lattices

SupramoleculeName: Structure of oocyte cytoplasmic lattices / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#16
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: F-box and WD-40 domain protein 19

MacromoleculeName: F-box and WD-40 domain protein 19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 53.657457 KDa
SequenceString: MEIHLPSLPM MKILSYLDAY SLLQAAKVNK NWNELASSDV LWRKLCQKRW LYCDRVTLQL HGLETWKQFF ISRTWQEHAK TRAKPEDFN YKEIPVAFEF RAHPCYISRH GLIRNGQGKS AVCMVTSTNR ISTWDVHEGA MTWVSPVQPS YITRMTTLPE M HIAVTIDM ...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

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Macromolecule #2: F-box and WD-40 domain protein 21

MacromoleculeName: F-box and WD-40 domain protein 21 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 54.517043 KDa
SequenceString: MEIHLPRLPL MEIFSYLDAY SLLQVAQVNK NWNELASSDV LWRKLCQKRW FYCNMVTQQL LGKETWKEFF IYRTWQEHAK SRAKPEDFI YKEIPAEYGI QAYACYISEH GLTRNGQGRS VICMATSMNR ISTWDIHEGV LTWVSPEQPA SIKLLTTLPE M YIAVTVDM ...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

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Macromolecule #3: Inactive protein-arginine deiminase type-6

MacromoleculeName: Inactive protein-arginine deiminase type-6 / type: protein_or_peptide / ID: 3 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 76.854109 KDa
SequenceString: MSFQNSLSLS LVNPTHALCM VGMEITLDIS KCAPDKCKSF TIRGSPRILI HISSSVIAGK EDTVVWRSMN HPTVALVRMV APSPTVDED KVLVSYFCPD QEVPTATAVL FLTGIEISLE ADIYRDGQLD MPSDKQAKKK WMWGMNGWGA ILLVNCSPNA V GQPDEQSF ...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

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

MacromoleculeName: NLR family, pyrin domain containing 4F / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 108.001281 KDa
SequenceString: MASFISDFGL IWYLRELNKK EFMKFKDFLI QEILELKLKQ VSSTKVKKAS REDLANLLLK CGENQAWDMT FRILQKINRK DLTERATGA IVGNPNLYRD HLKKKLTHDC PKKFNVRIQD FIKETFIQND YDAFENLLIS KGTERKPHMV FLKGMAGVGK T LMLKNLML ...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

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Macromolecule #5: Oocyte-expressed protein homolog

MacromoleculeName: Oocyte-expressed protein homolog / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.481295 KDa
SequenceString:
MASHTADADA KPDSDSQKLL NVLPVSLRLR TRPWWFPIQE VSNPLVLYME AWVAERVIGT DQAEISEIEW MCQALLTVDS VNSGNLAEI TIFGQPSAQT RMKNILLNMA AWHKENELQR AVKVKEVEEF LKIRASSILS KLSKKGLKLA GFPLPLEGRE T QMES

UniProtKB: Oocyte-expressed protein homolog

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Macromolecule #6: Isoform 2 of KH domain-containing protein 3

MacromoleculeName: Isoform 2 of 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 weightTheoretical: 37.854129 KDa
SequenceString: MASLKRFQTL VPLDHKQGTL FEIIGEPKLP KWFHVECLED PKRLYVEPRL LEIMFGKDGE HIPHLESMLH TLIHVNVWGP ERRAEIWIF GPPPFRRDVD RMLTDLAHYC RMKLMEIEAL EAGVERRRMA AHKAATQPAP VKVREAAPRP ASVKVPETAT Q PAPVKVRE ...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 ASVQESGRTE

UniProtKB: KH domain-containing protein 3

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Macromolecule #7: NACHT, LRR and PYD domains-containing protein 5

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 5 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 131.468547 KDa
SequenceString: MGPPEKESKA ILKARGLEEE QKSERKMTSP ENDSKSIQKD QGPEQEQTSE STMGPPEKES KAILKARGLE EEQKSERKMT SPENDSKSI QKDQGPEQEQ TSESTMGPPE KDSKAILKAR GLEEEQKSES TMSPSENVSR AILKDSGSEE VEQASERKMT S PENDSKSI ...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

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Macromolecule #8: Transducin-like enhancer protein 6

MacromoleculeName: 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 weightTheoretical: 65.187332 KDa
SequenceString: MTSHRQSSDT FGGILPSTLS SRYLSIVNQL PEEFSSVVSE MMVHLENIFS LAENFFQAIE RFSRTPDLLE RNKMSIGVGA EGDSWPCHV SHEAPMGSAQ TTENSAKEED KQVPESAALQ HPKFKSTPGP QLPTRRRFLS ESDELQDPQP VWDAEPQFCQ G FLIQGLWE ...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

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Macromolecule #9: Zinc finger BED domain-containing protein 3

MacromoleculeName: Zinc finger BED domain-containing protein 3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.643373 KDa
SequenceString: MKSKKPLKIT MEDSRRLNDP AEQGGLCPAP VGPSYSEAWG YFHLDPAQPR HRMMSAWATC RLCGLQVGGL PNFQMWTRAL CQHLSDVHL PELKKSAAPS SPTTMPCPPP PSPTMAAEGD WARLLEQMGE LAMRGSQREL ELERREAALM QAELELERKR Q ALKQEAQS ...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 #10: Tubulin beta-2A chain

MacromoleculeName: Tubulin beta-2A chain / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 49.953797 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...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 #11: Tubulin alpha-1C chain

MacromoleculeName: Tubulin alpha-1C chain / type: protein_or_peptide / ID: 11 / Number of copies: 2 / 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 weightTheoretical: 49.962172 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...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: Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: 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 weightTheoretical: 16.706133 KDa
SequenceString:
MALKRINKEL SDLARDPPAQ CSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSICSL LCDPNPDDPL VPEIARIYKT DRDKYNRISR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D3

+
Macromolecule #13: E3 ubiquitin-protein ligase UHRF1

MacromoleculeName: E3 ubiquitin-protein ligase UHRF1 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 88.436805 KDa
SequenceString: MWIQVRTMDG KETHTVNSLS RLTKVQELRK KIEEVFHVEP QLQRLFYRGK QMEDGHTLFD YDVRLNDTIQ LLVRQSLALP LSTKERDSE LSDSDSGYGV GHSESDKSST HGEGAAEADD KTVWEDTDLG LYKVNEYVDV RDNIFGAWFE AQVVQVQKRA L SEDEPCSS ...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

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

MacromoleculeName: NACHT, LRR and PYD domains-containing protein 14 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 113.527188 KDa
SequenceString: MKTEDDEMEY EASKEETVSE DKDFDDGIDY RTVIKENIFT MWYKTSLHGE FATLNCVITP KDQNLLQHIF DEDIQTSEAP QTVVLQGAA GIGKTTLLKK AVLEWADGNL YQQFTHVFYL NGKEISQVKE KSFAQLISKH WPSSEGPIEQ VLSKPSSLLF I IDSFDELD ...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 #15: S-phase kinase-associated protein 1

MacromoleculeName: S-phase kinase-associated protein 1 / type: protein_or_peptide / ID: 15 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.693992 KDa
SequenceString:
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 #16: Expressed sequence C85627

MacromoleculeName: Expressed sequence C85627 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 54.205703 KDa
SequenceString: METHLPSLPS LPMMKILSYL DAYSLLQVAQ VNKNWNALAS SDVLWRKLCQ KRWLYCDTVI LQLHDKETWK QFFVNRTYQE HTKTRAKPE DFTYKEICAE TGIWAYACYI SGRGLTRNGQ GTSVVCMLTS MTKISTWDIH EGVMTWVSPV QPTTIKLLNT L PEMHIAVT ...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 #17: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 17 / Number of copies: 5 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

+
Macromolecule #18: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 18 / Number of copies: 4 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

+
Macromolecule #19: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 19 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #20: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 20 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

16458

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 288673
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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