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- EMDB-28630: CX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations -

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Basic information

Entry
Database: EMDB / ID: EMD-28630
TitleCX3CR1 nucleosome and PU.1 complex containing disulfide bond mutations
Map data
Sample
  • Complex: nucleosome PU.1 mutant complex
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-C
    • Protein or peptide: Histone H2B type 2-E
    • Protein or peptide: Histone H2A type 2-C
    • Protein or peptide: Single-chain variable fragment
    • Protein or peptide: Transcription factor PU.1
Keywordsnucleosome / transcription factor / transcription / chromatin binding protein-DNA complex / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity ...positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / granulocyte differentiation / lymphocyte differentiation / apoptotic process involved in blood vessel morphogenesis / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation / immature B cell differentiation / negative regulation of MHC class II biosynthetic process / lymphoid progenitor cell differentiation / myeloid dendritic cell differentiation / vasculature development / regulation of DNA-binding transcription factor activity / oncogene-induced cell senescence / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / positive regulation of B cell differentiation / NFAT protein binding / somatic stem cell population maintenance / macrophage differentiation / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / cis-regulatory region sequence-specific DNA binding / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / lipopolysaccharide-mediated signaling pathway / nucleosomal DNA binding / protein sequestering activity / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / transcription initiation-coupled chromatin remodeling / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / transforming growth factor beta receptor signaling pathway / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / erythrocyte differentiation / PRC2 methylates histones and DNA / positive regulation of miRNA transcription / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / DNA-binding transcription repressor activity, RNA polymerase II-specific / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / structural constituent of chromatin / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization
Similarity search - Function
Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase ...Ets-domain signature 1. / ETS family / Ets-domain signature 2. / Ets domain / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / 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 H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcription factor PU.1 / Arachidonate 15-lipoxygenase / Histone H3.1 / Histone H2A type 2-C / Histone H2B type 2-E
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsLian T / Guan R / Bai Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα.
Authors: Tengfei Lian / Ruifang Guan / Bing-Rui Zhou / Yawen Bai /
Abstract: Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA ...Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remains elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp of entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome.
History
DepositionOct 20, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28630.png

Downloads & links

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Map

FileDownload / File: emd_28630.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.056 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-2.315202 - 4.248767
Average (Standard dev.)0.004105717 (±0.12015651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 253.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28630_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28630_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : nucleosome PU.1 mutant complex

EntireName: nucleosome PU.1 mutant complex
Components
  • Complex: nucleosome PU.1 mutant complex
    • DNA: DNA (167-MER)
    • DNA: DNA (167-MER)
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-C
    • Protein or peptide: Histone H2B type 2-E
    • Protein or peptide: Histone H2A type 2-C
    • Protein or peptide: Single-chain variable fragment
    • Protein or peptide: Transcription factor PU.1

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Supramolecule #1: nucleosome PU.1 mutant complex

SupramoleculeName: nucleosome PU.1 mutant complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.538973 KDa
SequenceString: (DT)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DA) (DG)(DG)(DA)(DA)(DC)(DC)(DC)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DC)(DC)(DT)(DG)(DT) (DG)(DT)(DC)(DT)(DG)(DC)(DA)(DA)(DG)(DT) (DA) (DC)(DA)(DG)(DA)(DA)(DC) ...String:
(DT)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DA) (DG)(DG)(DA)(DA)(DC)(DC)(DC)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DC)(DC)(DT)(DG)(DT) (DG)(DT)(DC)(DT)(DG)(DC)(DA)(DA)(DG)(DT) (DA) (DC)(DA)(DG)(DA)(DA)(DC)(DT)(DA) (DG)(DC)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DA) (DC)(DT) (DG)(DA)(DC)(DC)(DT)(DA)(DT) (DT)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DG)(DG) (DG)(DG)(DA) (DA)(DT)(DC)(DG)(DG)(DG) (DA)(DA)(DG)(DT)(DA)(DT)(DC)(DC)(DA)(DT) (DT)(DG)(DC)(DT) (DA)(DA)(DG)(DA)(DC) (DT)(DC)(DA)(DG)(DC)(DA)(DA)(DT)(DG)(DC) (DT)(DG)(DC)(DA)(DA) (DC)(DT)(DC)(DT) (DC)(DA)(DG)(DC)(DA)(DA)(DC)(DC)(DA)(DG) (DC)(DT)(DG)(DA)(DA)(DG) (DA)(DT)(DC) (DA)(DG)(DC)(DA)(DG)(DC)(DC)(DG)(DA)(DG) (DA)(DG)(DG)(DC)(DC)(DC)(DT) (DG)(DC) (DA)(DC)(DC)(DT)(DA)

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Macromolecule #2: DNA (167-MER)

MacromoleculeName: DNA (167-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 51.558816 KDa
SequenceString: (DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG)(DA) ...String:
(DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG)(DA)(DG)(DT) (DT)(DG)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DG) (DC)(DT) (DG)(DA)(DG)(DT)(DC)(DT)(DT) (DA)(DG)(DC)(DA)(DA)(DT)(DG)(DG)(DA)(DT) (DA)(DC)(DT) (DT)(DC)(DC)(DC)(DG)(DA) (DT)(DT)(DC)(DC)(DC)(DC)(DT)(DC)(DA)(DC) (DA)(DA)(DA)(DA) (DA)(DT)(DA)(DG)(DG) (DT)(DC)(DA)(DG)(DT)(DC)(DT)(DG)(DT)(DC) (DT)(DG)(DG)(DC)(DT) (DA)(DG)(DT)(DT) (DC)(DT)(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DC) (DA)(DG)(DA)(DC)(DA)(DC) (DA)(DG)(DG) (DG)(DC)(DA)(DT)(DG)(DT)(DG)(DG)(DG)(DG) (DT)(DT)(DC)(DC)(DT)(DA)(DT) (DT)(DT) (DT)(DT)(DC)(DT)(DA)

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Macromolecule #3: Histone H3.1

MacromoleculeName: Histone H3.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.437167 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.1

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Arachidonate 15-lipoxygenase

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Macromolecule #5: Histone H2A type 2-C

MacromoleculeName: Histone H2A type 2-C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.019467 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKCRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHKAKSK

UniProtKB: Histone H2A type 2-C

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Macromolecule #6: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.951239 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

UniProtKB: Histone H2B type 2-E

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Macromolecule #7: Histone H2A type 2-C

MacromoleculeName: Histone H2A type 2-C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.017428 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHKAKSK

UniProtKB: Histone H2A type 2-C

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Macromolecule #8: Single-chain variable fragment

MacromoleculeName: Single-chain variable fragment / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 29.030146 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ...String:
MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ASLGERVTIT CKASQDIRSY LSWYQQKPWK SPKTLIYYAT SLADGVPSRF SGSGSGQDFS LTINNLESDD TA TYYCLQH GESPYTFGSG TKLEIKRA

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Macromolecule #9: Transcription factor PU.1

MacromoleculeName: Transcription factor PU.1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 32.865844 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGMLQACKM EGFSLTAPPS DDLVTYDSEL YQRPMHDYYS FVGSDGESHS DHYWDFSAHH VHNNEFENFP ENHFTELQS VQPPQLQQLY RHMELEQMHV LDTPMVPPHT GLSHQVSYMP RMCFPYQTLS PAHQQSSDEE EGERQSPPLE V SDGEADGL ...String:
MGSSHHHHHH SSGMLQACKM EGFSLTAPPS DDLVTYDSEL YQRPMHDYYS FVGSDGESHS DHYWDFSAHH VHNNEFENFP ENHFTELQS VQPPQLQQLY RHMELEQMHV LDTPMVPPHT GLSHQVSYMP RMCFPYQTLS PAHQQSSDEE EGERQSPPLE V SDGEADGL EPGPGLLHGE TGSKKKIRLY QFLLDLLRSG DMKDSIWWVD KDKGTFQFSS KHKEALAHRW GIQKCNRKKM TY QKMARAL RNYGKTGEVK KVKKKLTYQF SGEVLGRGGL AERRLPPH

UniProtKB: Transcription factor PU.1

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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: 7.3
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: 53.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 127327
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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