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- EMDB-26258: structure of LIN28b nucleosome bound 3 OCT4 -

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Basic information

Entry
Database: EMDB / ID: EMD-26258
Titlestructure of LIN28b nucleosome bound 3 OCT4
Map data
Sample
  • Complex: Complex of nucleosome bound to three OCT-4s
    • 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
    • DNA: DNA (162-MER)
    • DNA: DNA (162-MER)
    • Protein or peptide: Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
    • Protein or peptide: Single-chain variable fragment
Keywordsnucleosome / transcription factor / transcription / CHROMATIN BINDING PROTEIN-DNA complex / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation ...cell fate commitment involved in formation of primary germ layer / cardiac cell fate determination / POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation / Formation of the anterior neural plate / endodermal-mesodermal cell signaling / regulation of asymmetric cell division / endodermal cell fate specification / Specification of primordial germ cells / heart induction / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / Specification of the neural plate border / Transcriptional regulation of pluripotent stem cells / Germ layer formation at gastrulation / miRNA binding / somatic stem cell population maintenance / blastocyst development / carbohydrate transmembrane transporter activity / anatomical structure morphogenesis / negative regulation of megakaryocyte differentiation / BMP signaling pathway / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / negative regulation of miRNA transcription / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / HCMV Late Events / innate immune response in mucosa / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / heterochromatin formation / PKMTs methylate histone lysines / Metalloprotease DUBs / Meiotic recombination / DNA-binding transcription repressor activity, RNA polymerase II-specific / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / response to wounding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / UCH proteinases / sequence-specific double-stranded DNA binding / antimicrobial humoral immune response mediated by antimicrobial peptide / nucleosome / positive regulation of canonical Wnt signaling pathway / nucleosome assembly / antibacterial humoral response / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Processing of DNA double-strand break ends / outer membrane-bounded periplasmic space / gene expression / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / Oxidative Stress Induced Senescence / RNA polymerase II-specific DNA-binding transcription factor binding / Estrogen-dependent gene expression / transcription regulator complex / sequence-specific DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding
Similarity search - Function
POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. ...POU-specific domain / POU domain / Pou domain - N-terminal to homeobox domain / POU-specific (POUs) domain signature 1. / POU-specific (POUs) domain signature 2. / POU-specific (POUs) domain profile. / Found in Pit-Oct-Unc transcription factors / : / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Lambda repressor-like, DNA-binding domain superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / 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 H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Homeobox-like domain superfamily / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Maltodextrin-binding protein / Histone H4 / Histone H3.1 / POU domain, class 5, transcription factor 1 / Histone H2A type 2-C / Histone H2B type 2-E
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 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: Mol Cell / Year: 2023
Title: Structural mechanism of LIN28B nucleosome targeting by OCT4.
Authors: Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / David Wheeler / Yawen Bai /
Abstract: Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of ...Pioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize the in vivo nucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing human LIN28B DNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA sequences. Two use their POUS domains while the other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Our analysis of previous genomic data and determination of the ESRRB-nucleosome-OCT4 structure confirmed the generality of these structural features. Moreover, biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing the LIN28B nucleosome. Thus, our study suggests a mechanism of how OCT4 can target the nucleosome and open closed chromatin.
History
DepositionFeb 18, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26258.png

Downloads & links

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Map

FileDownload / File: emd_26258.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.056 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.93431157 - 2.4778302
Average (Standard dev.)0.0049446863 (±0.06710585)
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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Sample components

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Entire : Complex of nucleosome bound to three OCT-4s

EntireName: Complex of nucleosome bound to three OCT-4s
Components
  • Complex: Complex of nucleosome bound to three OCT-4s
    • 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
    • DNA: DNA (162-MER)
    • DNA: DNA (162-MER)
    • Protein or peptide: Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
    • Protein or peptide: Single-chain variable fragment

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Supramolecule #1: Complex of nucleosome bound to three OCT-4s

SupramoleculeName: Complex of nucleosome bound to three OCT-4s / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.1

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

UniProtKB: Histone H3.1

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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: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 2-C

MacromoleculeName: Histone H2A type 2-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.017428 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #4: Histone H2B type 2-E

MacromoleculeName: Histone H2B type 2-E / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.951239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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: Maltodextrin-binding protein,POU domain, class 5, transcription f...

MacromoleculeName: Maltodextrin-binding protein,POU domain, class 5, transcription factor 1
type: protein_or_peptide / ID: 7 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.269703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKEAKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY F TWPLIAAD ...String:
MKEAKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY F TWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LVDLIKNKHM NADTDYSIAE AAFNKGETAM TINGPWAWSN ID TSKVNYG VTVLP(UNK)FKGQ PSKPFVGVLS AGINAASPNK ELAKEFLENY LLTDEGLEAV NKDKPLGAVA LKSYEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQTVDAALA AAQTNAGSEN LYFQGSVDSA AASDIKALQK ELEQFAKLL KQKRITLGYT QADVGLTLGV LFGKVFSQTT ICRFEALQLS FKNMCKLRPL LQKWVEEADN NENLQEICKA E TLVQARKR KRTSIENRVR GNLENLFLQC PKPTLQQISH IAQQLGLEKD VVRVWFCNRR QKGKRSSSEF HHHHHH

UniProtKB: Maltodextrin-binding protein, POU domain, class 5, transcription factor 1

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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: Mus musculus (house mouse)
Molecular weightTheoretical: 29.030146 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 #5: DNA (162-MER)

MacromoleculeName: DNA (162-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.398344 KDa
SequenceString: (DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT)(DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT)(DG) (DG) (DA)(DA)(DC)(DT)(DT)(DA) ...String:
(DA)(DG)(DT)(DG)(DG)(DT)(DA)(DT)(DT)(DA) (DA)(DC)(DA)(DT)(DA)(DT)(DC)(DC)(DT)(DC) (DA)(DG)(DT)(DG)(DG)(DT)(DG)(DA)(DG) (DT)(DA)(DT)(DT)(DA)(DA)(DC)(DA)(DT)(DG) (DG) (DA)(DA)(DC)(DT)(DT)(DA)(DC)(DT) (DC)(DC)(DA)(DA)(DC)(DA)(DA)(DT)(DA)(DC) (DA)(DG) (DA)(DT)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA)(DA)(DA)(DT)(DG)(DT)(DA)(DG) (DT)(DC)(DT) (DA)(DA)(DG)(DT)(DG)(DA) (DA)(DG)(DG)(DA)(DA)(DG)(DA)(DA)(DG)(DG) (DA)(DA)(DA)(DG) (DG)(DT)(DG)(DG)(DG) (DA)(DG)(DC)(DT)(DG)(DC)(DC)(DA)(DT)(DC) (DA)(DC)(DT)(DC)(DA) (DG)(DA)(DA)(DT) (DT)(DG)(DT)(DC)(DC)(DA)(DG)(DC)(DA)(DG) (DG)(DG)(DA)(DT)(DT)(DG) (DT)(DG)(DC) (DA)(DA)(DG)(DC)(DT)(DT)(DG)(DT)(DG)(DA) (DA)(DT)(DA)(DA)(DA)(DG)(DA) (DC)(DA)

GENBANK: GENBANK: Z95329.1

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Macromolecule #6: DNA (162-MER)

MacromoleculeName: DNA (162-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.59568 KDa
SequenceString: (DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG) (DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA)(DA) (DT) (DT)(DC)(DT)(DG)(DA)(DG) ...String:
(DT)(DG)(DT)(DC)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DC)(DA)(DA)(DG)(DC)(DT)(DT)(DG) (DC)(DA)(DC)(DA)(DA)(DT)(DC)(DC)(DC) (DT)(DG)(DC)(DT)(DG)(DG)(DA)(DC)(DA)(DA) (DT) (DT)(DC)(DT)(DG)(DA)(DG)(DT)(DG) (DA)(DT)(DG)(DG)(DC)(DA)(DG)(DC)(DT)(DC) (DC)(DC) (DA)(DC)(DC)(DT)(DT)(DT)(DC) (DC)(DT)(DT)(DC)(DT)(DT)(DC)(DC)(DT)(DT) (DC)(DA)(DC) (DT)(DT)(DA)(DG)(DA)(DC) (DT)(DA)(DC)(DA)(DT)(DT)(DT)(DA)(DT)(DT) (DC)(DA)(DG)(DC) (DA)(DT)(DC)(DT)(DG) (DT)(DA)(DT)(DT)(DG)(DT)(DT)(DG)(DG)(DA) (DG)(DT)(DA)(DA)(DG) (DT)(DT)(DC)(DC) (DA)(DT)(DG)(DT)(DT)(DA)(DA)(DT)(DA)(DC) (DT)(DC)(DA)(DC)(DC)(DA) (DC)(DT)(DG) (DA)(DG)(DG)(DA)(DT)(DA)(DT)(DG)(DT)(DT) (DA)(DA)(DT)(DA)(DC)(DC)(DA) (DC)(DT)

GENBANK: GENBANK: Z95329.1

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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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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