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- PDB-9t67: Cytoplasmic lattice filament repeat unit with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 9t67
TitleCytoplasmic lattice filament repeat unit with ubiquitin
Components
  • (NACHT, LRR and PYD domains-containing protein ...) x 2
  • E3 ubiquitin-protein ligase UHRF1
  • F-box/WD repeat-containing protein
  • Inactive protein-arginine deiminase type-6
  • KH domain-containing protein 3
  • NLR family, pyrin domain containing 4F
  • Oocyte-expressed protein homolog
  • Polyubiquitin-C
  • S-phase kinase-associated protein 1
  • Transducin-like enhancer protein 6
  • Tubulin alpha-1C chain
  • Tubulin beta-4B chain
  • Ubiquitin-conjugating enzyme E2 D3
  • Zinc finger BED domain-containing protein 3
KeywordsUNKNOWN FUNCTION / Ubiquitination / Complex / Filament
Function / homology
Function and homology information


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 ...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
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 / UHRF1/2-like ...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.
Similarity search - Domain/homology
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 ...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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.7 Å
AuthorsSingh, K. / Harasimov, K. / Carter, A.
Funding support United Kingdom, European Union, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_A025_1011 United Kingdom
European Molecular Biology Organization (EMBO)ALTF 426-2023European Union
Wellcome Trust221856/Z/20/Z United Kingdom
CitationJournal: 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 ...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
DepositionNov 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: KH domain-containing protein 3
1: Inactive protein-arginine deiminase type-6
2: Inactive protein-arginine deiminase type-6
3: Inactive protein-arginine deiminase type-6
4: NACHT, LRR and PYD domains-containing protein 5
5: Transducin-like enhancer protein 6
6: Oocyte-expressed protein homolog
7: NACHT, LRR and PYD domains-containing protein 5
8: Transducin-like enhancer protein 6
9: Oocyte-expressed protein homolog
A: Inactive protein-arginine deiminase type-6
AA: Zinc finger BED domain-containing protein 3
AE: NLR family, pyrin domain containing 4F
AF: NLR family, pyrin domain containing 4F
AG: NACHT, LRR and PYD domains-containing protein 14
AH: E3 ubiquitin-protein ligase UHRF1
AI: Ubiquitin-conjugating enzyme E2 D3
AJ: Tubulin alpha-1C chain
AK: Tubulin beta-4B chain
AL: F-box/WD repeat-containing protein
AM: S-phase kinase-associated protein 1
AN: F-box/WD repeat-containing protein
AO: S-phase kinase-associated protein 1
B: Inactive protein-arginine deiminase type-6
C: Inactive protein-arginine deiminase type-6
D: Inactive protein-arginine deiminase type-6
E: Inactive protein-arginine deiminase type-6
F: Inactive protein-arginine deiminase type-6
G: Inactive protein-arginine deiminase type-6
H: Inactive protein-arginine deiminase type-6
I: Inactive protein-arginine deiminase type-6
J: Inactive protein-arginine deiminase type-6
K: Inactive protein-arginine deiminase type-6
L: Inactive protein-arginine deiminase type-6
M: NACHT, LRR and PYD domains-containing protein 5
N: Transducin-like enhancer protein 6
O: Oocyte-expressed protein homolog
P: NACHT, LRR and PYD domains-containing protein 5
Q: Transducin-like enhancer protein 6
R: Oocyte-expressed protein homolog
S: KH domain-containing protein 3
T: Zinc finger BED domain-containing protein 3
U: Polyubiquitin-C
V: Polyubiquitin-C
W: Polyubiquitin-C
X: NLR family, pyrin domain containing 4F
Y: NLR family, pyrin domain containing 4F
Z: NACHT, LRR and PYD domains-containing protein 14
a: E3 ubiquitin-protein ligase UHRF1
b: Ubiquitin-conjugating enzyme E2 D3
c: Tubulin alpha-1C chain
d: Tubulin beta-4B chain
e: F-box/WD repeat-containing protein
f: S-phase kinase-associated protein 1
g: F-box/WD repeat-containing protein
h: S-phase kinase-associated protein 1
m: Inactive protein-arginine deiminase type-6
n: NACHT, LRR and PYD domains-containing protein 14
o: E3 ubiquitin-protein ligase UHRF1
p: Ubiquitin-conjugating enzyme E2 D3
q: Tubulin alpha-1C chain
r: Tubulin beta-4B chain
s: Inactive protein-arginine deiminase type-6
t: Inactive protein-arginine deiminase type-6
u: Inactive protein-arginine deiminase type-6
v: Inactive protein-arginine deiminase type-6
w: Inactive protein-arginine deiminase type-6
x: Inactive protein-arginine deiminase type-6
y: Inactive protein-arginine deiminase type-6
z: Inactive protein-arginine deiminase type-6


Theoretical massNumber of molelcules
Total (without water)4,499,19470
Polymers4,499,19470
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 13 types, 63 molecules 0S123ABCDEFGHIJKLmstuvwxyz58NQ...

#1: Protein KH domain-containing protein 3 / Protein Filia


Mass: 48055.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWU5
#2: Protein ...
Inactive protein-arginine deiminase type-6 / Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine ...Arginine deiminase-like protein / Egg and embryo abundant PAD / ePAD / P75 / Peptidylarginine deiminase VI / Protein-arginine deiminase type VI / Protein-arginine deiminase type-6


Mass: 76854.109 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K3V4
#4: Protein
Transducin-like enhancer protein 6 / Groucho-related protein 6


Mass: 65187.332 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WVB3
#5: Protein
Oocyte-expressed protein homolog / Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific ...Factor located in oocytes permitting embryonic development / Floped / Oocyte- and embryo-specific protein 19 / mOEP19 / STAT3 downstream gene and differentiation regulator


Mass: 18481.295 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CWE6
#6: Protein Zinc finger BED domain-containing protein 3 / Axin-interacting protein


Mass: 25643.373 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9D0L1
#7: Protein
NLR family, pyrin domain containing 4F


Mass: 108001.281 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: L7N1W9
#9: Protein E3 ubiquitin-protein ligase UHRF1 / Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / ...Nuclear protein 95 / Nuclear zinc finger protein Np95 / RING-type E3 ubiquitin transferase UHRF1 / Ubiquitin-like PHD and RING finger domain-containing protein 1 / mUhrf1 / Ubiquitin-like-containing PHD and RING finger domains protein 1


Mass: 88436.805 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: Q8VDF2, RING-type E3 ubiquitin transferase
#10: Protein Ubiquitin-conjugating enzyme E2 D3 / (E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / ...(E3-independent) E2 ubiquitin-conjugating enzyme D3 / E2 ubiquitin-conjugating enzyme D3 / Ubiquitin carrier protein D3 / Ubiquitin-conjugating enzyme E2(17)KB 3 / Ubiquitin-conjugating enzyme E2-17 kDa 3 / Ubiquitin-protein ligase D3


Mass: 16706.133 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P61079, E2 ubiquitin-conjugating enzyme, (E3-independent) E2 ubiquitin-conjugating enzyme
#11: Protein Tubulin alpha-1C chain / Alpha-tubulin 6 / Alpha-tubulin isotype M-alpha-6 / Tubulin alpha-6 chain


Mass: 49962.172 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
References: UniProt: P68373, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#12: Protein Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 49877.824 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P68372
#13: Protein
F-box/WD repeat-containing protein


Mass: 39676.895 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#14: Protein
S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / S-phase kinase-associated protein 1A / p19A / p19skp1


Mass: 18693.992 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9WTX5
#15: Protein Polyubiquitin-C


Mass: 8576.831 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P0CG50

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NACHT, LRR and PYD domains-containing protein ... , 2 types, 7 molecules 47MPAGZn

#3: Protein
NACHT, LRR and PYD domains-containing protein 5 / Maternal antigen that embryos require / Mater protein / Ooplasm-specific protein 1 / OP1


Mass: 131468.547 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9R1M5
#8: Protein NACHT, LRR and PYD domains-containing protein 14 / NALP-iota / Germ cell specific leucine-rich repeat NTPase


Mass: 113527.188 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q6B966

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Details

Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Multi-subunit complex of cytoplasmic lattice repeat unit with bound ubiquitin
Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 3.5 e/Å2 / Avg electron dose per subtomogram: 115 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION5.1volume selection
13RELION5.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30490 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 1153 / Num. of volumes extracted: 134387

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