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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 / germinal center B cell differentiation / negative regulation of neutrophil degranulation / 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 / germinal center B cell differentiation / negative regulation of neutrophil degranulation / 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 / negative regulation of MHC class II biosynthetic process / immature B cell differentiation / lymphoid progenitor cell differentiation / myeloid dendritic cell differentiation / vasculature development / oncogene-induced cell senescence / regulation of DNA-binding transcription factor activity / positive regulation of p38MAPK cascade / negative regulation of protein localization to chromatin / positive regulation of B cell differentiation / NFAT protein binding / macrophage differentiation / somatic stem cell population maintenance / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / cis-regulatory region sequence-specific DNA binding / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / transforming growth factor beta receptor signaling pathway / Assembly of the ORC complex at the origin of replication / transcription initiation-coupled chromatin remodeling / protein sequestering activity / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / lipopolysaccharide-mediated signaling pathway / Condensation of Prophase Chromosomes / erythrocyte differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / positive regulation of miRNA transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / histone deacetylase binding / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / structural constituent of chromatin / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / : / Histone H2B signature. / Histone H2B ...Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / : / 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 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / 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 / Histone H4 / 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-
UpdateOct 23, 2024-
Current statusOct 23, 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 253.44 Å		1.06 Å/pix.
x 240 pix.
= 253.44 Å		1.06 Å/pix.
x 240 pix.
= 253.44 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
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
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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: Histone H4

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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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