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- EMDB-38101: Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n... -

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Entry
Database: EMDB / ID: EMD-38101
TitleCryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
Map data
Sample
  • Complex: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • Protein or peptide: Histone H2A type 1-B/E
    • DNA: DNA (143-MER)
    • DNA: DNA (143-MER)
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
    • Protein or peptide: E3 ubiquitin-protein ligase RNF168
  • Ligand: ZINC ION
KeywordsRNF168 / nucleosome / H2AK13/15 ubiquitination / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / positive regulation of protein targeting to mitochondrion ...histone H2AK15 ubiquitin ligase activity / histone ubiquitin ligase activity / (E3-independent) E2 ubiquitin-conjugating enzyme / Signaling by BMP / protein K6-linked ubiquitination / isotype switching / double-strand break repair via classical nonhomologous end joining / protein K11-linked ubiquitination / DNA repair-dependent chromatin remodeling / positive regulation of protein targeting to mitochondrion / E2 ubiquitin-conjugating enzyme / response to ionizing radiation / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of transcription elongation by RNA polymerase II / protein monoubiquitination / ubiquitin conjugating enzyme activity / protein K63-linked ubiquitination / negative regulation of BMP signaling pathway / negative regulation of megakaryocyte differentiation / nucleosome binding / protein autoubiquitination / protein K48-linked ubiquitination / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / interstrand cross-link repair / Replacement of protamines by nucleosomes in the male pronucleus / SUMOylation of DNA damage response and repair proteins / CENP-A containing nucleosome / Packaging Of Telomere Ends / ubiquitin ligase complex / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / telomere organization / Meiotic synapsis / positive regulation of DNA repair / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / TICAM1, RIP1-mediated IKK complex recruitment / DNA methylation / Regulation of endogenous retroelements by KRAB-ZFP proteins / Condensation of Prophase Chromosomes / PINK1-PRKN Mediated Mitophagy / IKK complex recruitment mediated by RIP1 / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / innate immune response in mucosa / ubiquitin binding / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / Negative regulators of DDX58/IFIH1 signaling / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Peroxisomal protein import / Transcriptional regulation by small RNAs / Regulation of TNFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Formation of the beta-catenin:TCF transactivating complex / RING-type E3 ubiquitin transferase / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / protein modification process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / B-WICH complex positively regulates rRNA expression / Inactivation of CSF3 (G-CSF) signaling / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / double-strand break repair via nonhomologous end joining / HCMV Early Events / Transcriptional regulation of granulopoiesis / protein polyubiquitination / ubiquitin-protein transferase activity / structural constituent of chromatin / UCH proteinases / ubiquitin protein ligase activity / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / double-strand break repair / Antigen processing: Ubiquitination & Proteasome degradation
Similarity search - Function
E3 ubiquitin-protein ligase RNF168 / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. ...E3 ubiquitin-protein ligase RNF168 / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Ring finger / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Zinc finger RING-type profile. / Zinc finger, RING-type / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H2B type 1-K / Histone H2A type 1-B/E / Ubiquitin-conjugating enzyme E2 D3 / Histone H4 / Histone H3.2 / E3 ubiquitin-protein ligase RNF168
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsAi HS / Tong ZB / Deng ZH / Pan M / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810 for L. Liu, and 22277073 for M. Pan China
CitationJournal: Biorxiv / Year: 2024
Title: Capturing Snapshots of Nucleosomal H2A K13/K15 Ubiquitination Mediated by the Monomeric E3 Ligase RNF168
Authors: Ai H / Tong Z / Deng Z / Shi Q / Tao S / Liang J / Sun M / Wu X / Zheng Q / Liang L / Li JB / Gao S / Tian C / Liu L / Pan M
History
DepositionNov 24, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38101.png

Downloads & links

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Map

FileDownload / File: emd_38101.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.022449065 - 0.06863741
Average (Standard dev.)0.00021433667 (±0.0019520313)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38101_msk_1.map
Projections & Slices
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Additional map: Cryo-EM map of RNF168/UbcH5c-Ub/monoubiquitinated nucleosome complex at a...

Fileemd_38101_additional_1.map
AnnotationCryo-EM map of RNF168/UbcH5c-Ub/monoubiquitinated nucleosome complex at a resolution of 6.2 angstrom
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_38101_half_map_1.map
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Half map: #2

Fileemd_38101_half_map_2.map
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Sample components

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Entire : cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n...

EntireName: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
Components
  • Complex: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-K
    • Protein or peptide: Histone H2A type 1-B/E
    • DNA: DNA (143-MER)
    • DNA: DNA (143-MER)
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 D3
    • Protein or peptide: E3 ubiquitin-protein ligase RNF168
  • Ligand: ZINC ION

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Supramolecule #1: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub n...

SupramoleculeName: cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by activity-based chemical trapping strategy (adjacent H2AK13/15 dual-monoubiquitination)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.401268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PHRYRPGTVA LREIRRYQKS TELLIRKLPF QRLVREIAQD FKTDLRFQSS AVMALQEASE AYLVGLFEDT NLSAIHAKRV TIMPKDIQL ARRIRGER

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.352003 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVYA LKRQGRTLYG FG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.482382 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ACTRSSRAGL QFPVGRVHRL LRKGNYSERV GAGAPVYLAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAIRNDEEL NKLLGRVTI AQGGVLPNIQ AVLLPK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #4: Histone H2B type 1-K

MacromoleculeName: Histone H2B type 1-K / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.477994 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTSA

UniProtKB: Histone H2B type 1-K

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Macromolecule #5: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.807769 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIRN DEELNKLLG RVTIAQGGVL PNIQAVLLP

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #8: Ubiquitin-conjugating enzyme E2 D3

MacromoleculeName: Ubiquitin-conjugating enzyme E2 D3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.657938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALKRINKEL SDLARDPPAQ SSAGPVGDDM FHWQATIMGP NDSPYQGGVF FLTIHFPTDY PFKPPKVAFT TRIYHPNINS NGSICLDIL RSQWSPALTI SKVLLSISSL LSDPNPDDPL VPEIARIYKT DRDKYNRISR EWTQKYAM

UniProtKB: Ubiquitin-conjugating enzyme E2 D3

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Macromolecule #9: E3 ubiquitin-protein ligase RNF168

MacromoleculeName: E3 ubiquitin-protein ligase RNF168 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.987123 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MALPKDAIPS LSECQCGICM EILVEPVTLP CNHTLCKPCF QSTVEKASLC CPFCRRRVSS WTRYHTRRNS LVNVELWTII QKHYPRECK LRASGQESEE VADDYQPVRL LSKP

UniProtKB: E3 ubiquitin-protein ligase RNF168

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Macromolecule #6: DNA (143-MER)

MacromoleculeName: DNA (143-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.359242 KDa
SequenceString: (DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC) ...String:
(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA) (DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG) (DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG)(DA) (DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT)(DA) (DA)(DA) (DA)(DC)(DG)(DC)(DG)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC)(DG) (DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT) (DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT)(DG) (DC)(DT)(DA)(DG) (DA)(DG)(DC)(DT)(DG) (DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC)(DA) (DA)(DT)(DT)(DG)(DA) (DG)(DC)(DG)(DG) (DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG)(DA)(DT)(DT) (DC)(DT)(DC)

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Macromolecule #7: DNA (143-MER)

MacromoleculeName: DNA (143-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.918973 KDa
SequenceString: (DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG) (DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT) (DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC) (DA) (DG)(DC)(DT)(DC)(DT)(DA) ...String:
(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG) (DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC) (DC)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT) (DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC) (DA) (DG)(DC)(DT)(DC)(DT)(DA)(DG)(DC) (DA)(DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA) (DC)(DG) (DC)(DA)(DC)(DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC) (DC)(DC)(DG) (DC)(DG)(DT)(DT)(DT)(DT) (DA)(DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG) (DG)(DG)(DG)(DA) (DT)(DT)(DA)(DC)(DT) (DC)(DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC) (DC)(DA)(DG)(DG)(DC) (DA)(DC)(DG)(DT) (DG)(DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DC)(DA)(DT)(DC) (DC)(DT)(DG)

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Macromolecule #10: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 10 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147576
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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