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- EMDB-43196: Cryo-EM structure of GATA4 in complex with ALBN1 nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-43196
TitleCryo-EM structure of GATA4 in complex with ALBN1 nucleosome
Map datamain map
Sample
  • Complex: GATA4 in complex with 186bp ALBN1 nucleosome
    • DNA: DNA (159-MER)
    • DNA: DNA (159-MER)
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4
  • Ligand: ZINC ION
Keywordsnucleosome / pioneer transcription factors / DNA binding proteins / transcription / chromatin / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex
Function / homology
Function and homology information


atrial septum secundum morphogenesis / atrioventricular valve formation / embryonic heart tube anterior/posterior pattern specification / transdifferentiation / Formation of lateral plate mesoderm / cardiac right ventricle morphogenesis / intestinal epithelial cell differentiation / atrioventricular node development / co-SMAD binding / atrial septum morphogenesis ...atrial septum secundum morphogenesis / atrioventricular valve formation / embryonic heart tube anterior/posterior pattern specification / transdifferentiation / Formation of lateral plate mesoderm / cardiac right ventricle morphogenesis / intestinal epithelial cell differentiation / atrioventricular node development / co-SMAD binding / atrial septum morphogenesis / cardiac muscle tissue regeneration / cell growth involved in cardiac muscle cell development / Transcriptional regulation of testis differentiation / cardiac ventricle morphogenesis / endocardial cushion development / Physiological factors / atrial septum primum morphogenesis / atrioventricular canal development / embryonic foregut morphogenesis / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / Formation of definitive endoderm / endoderm development / positive regulation of BMP signaling pathway / Developmental Lineage of Pancreatic Acinar Cells / response to vitamin A / aortic valve morphogenesis / regulation of cardiac muscle cell contraction / Cardiogenesis / negative regulation of cardiac muscle cell apoptotic process / ventricular septum development / DNA-binding transcription activator activity / NFAT protein binding / detection of maltose stimulus / heart looping / maltose transport complex / carbohydrate transport / negative regulation of apoptotic signaling pathway / positive regulation of vascular endothelial growth factor production / carbohydrate transmembrane transporter activity / cell fate commitment / maltose binding / negative regulation of tumor necrosis factor-mediated signaling pathway / maltose transport / maltodextrin transmembrane transport / response to mechanical stimulus / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / telomere organization / Interleukin-7 signaling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / negative regulation of autophagy / Assembly of the ORC complex at the origin of replication / ATP-binding cassette (ABC) transporter complex / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / epigenetic regulation of gene expression / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / innate immune response in mucosa / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / cell chemotaxis / HDMs demethylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / cellular response to glucose stimulus / lipopolysaccharide binding / Transcriptional regulation by small RNAs / wound healing / 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 / Metalloprotease DUBs / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines
Similarity search - Function
GATA-type transcription activator, N-terminal / Transcription factor GATA-4/5/6 / GATA-type transcription activator, N-terminal / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...GATA-type transcription activator, N-terminal / Transcription factor GATA-4/5/6 / GATA-type transcription activator, N-terminal / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / 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 H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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 / Zinc finger, NHR/GATA-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2A type 1-B/E / Histone H2B type 1-J / Maltose/maltodextrin-binding periplasmic protein / Transcription factor GATA-4 / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsZhou BR / Bai Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)Intramural Research Program United States
CitationJournal: Mol Cell / Year: 2024
Title: Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4.
Authors: Bing-Rui Zhou / Hanqiao Feng / Furong Huang / Iris Zhu / Stephanie Portillo-Ledesma / Dan Shi / Kenneth S Zaret / Tamar Schlick / David Landsman / Qianben Wang / Yawen Bai /
Abstract: Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), ...Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), we determined the structures of the free N1 nucleosome and its complexes with FOXA1 and GATA4, both individually and in combination. We found that the DNA-binding domains of FOXA1 and GATA4 mainly recognize the linker DNA and an internal site in the nucleosome, respectively, whereas their intrinsically disordered regions interact with the acidic patch on histone H2A-H2B. FOXA1 efficiently enhances GATA4 binding by repositioning the N1 nucleosome. In vivo DNA editing and bioinformatics analyses suggest that the co-binding mode of FOXA1 and GATA4 plays important roles in regulating genes involved in liver cell functions. Our results reveal the mechanism whereby FOXA1 and GATA4 cooperatively bind to the nucleosome through nucleosome repositioning, opening chromatin by bending linker DNA and obstructing nucleosome packing.
History
DepositionDec 22, 2023-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43196.png

Downloads & links

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Map

FileDownload / File: emd_43196.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 316.8 Å		1.06 Å/pix.
x 300 pix.
= 316.8 Å		1.06 Å/pix.
x 300 pix.
= 316.8 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: 0.35
Minimum - Maximum-2.4211094 - 4.8585286
Average (Standard dev.)0.0014435083 (±0.107828)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_43196_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_43196_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GATA4 in complex with 186bp ALBN1 nucleosome

EntireName: GATA4 in complex with 186bp ALBN1 nucleosome
Components
  • Complex: GATA4 in complex with 186bp ALBN1 nucleosome
    • DNA: DNA (159-MER)
    • DNA: DNA (159-MER)
    • Protein or peptide: Histone H3.1
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4
  • Ligand: ZINC ION

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Supramolecule #1: GATA4 in complex with 186bp ALBN1 nucleosome

SupramoleculeName: GATA4 in complex with 186bp ALBN1 nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (159-MER)

MacromoleculeName: DNA (159-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.399637 KDa
SequenceString: (DA)(DT)(DC)(DC)(DG)(DA)(DG)(DA)(DT)(DG) (DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DC)(DC)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DC)(DA)(DG)(DC)(DA)(DG) (DG) (DG)(DC)(DA)(DC)(DT)(DG) ...String:
(DA)(DT)(DC)(DC)(DG)(DA)(DG)(DA)(DT)(DG) (DG)(DT)(DA)(DC)(DT)(DT)(DT)(DG)(DT)(DG) (DT)(DC)(DT)(DC)(DC)(DT)(DG)(DC)(DT) (DC)(DT)(DG)(DT)(DC)(DA)(DG)(DC)(DA)(DG) (DG) (DG)(DC)(DA)(DC)(DT)(DG)(DT)(DA) (DC)(DT)(DT)(DG)(DC)(DT)(DG)(DA)(DT)(DA) (DC)(DC) (DA)(DG)(DG)(DG)(DA)(DA)(DT) (DG)(DT)(DT)(DT)(DG)(DT)(DT)(DC)(DT)(DT) (DA)(DA)(DA) (DT)(DA)(DC)(DC)(DA)(DT) (DC)(DA)(DT)(DT)(DC)(DC)(DG)(DG)(DA)(DC) (DG)(DT)(DG)(DT) (DT)(DT)(DG)(DC)(DC) (DT)(DT)(DG)(DG)(DC)(DC)(DA)(DG)(DT)(DT) (DT)(DT)(DC)(DC)(DA) (DT)(DG)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DG)(DA)(DA)(DA) (DG)(DA)(DA)(DG)(DT)(DT) (DT)(DG)(DG) (DA)(DC)(DT)(DG)(DA)(DT)(DC)(DA)(DA)(DT) (DA)(DC)(DA)(DG)(DT)(DC)(DC) (DT)(DC) (DT)(DG)(DC)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DC)(DA)(DA)(DT)(DA)(DG)(DG) (DA) (DA)(DA)(DG)(DA)(DT)

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Macromolecule #2: DNA (159-MER)

MacromoleculeName: DNA (159-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.42777 KDa
SequenceString: (DA)(DT)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DA) (DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG)(DA) (DC)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DT) (DC) (DA)(DG)(DT)(DC)(DC)(DA) ...String:
(DA)(DT)(DC)(DT)(DT)(DT)(DC)(DC)(DT)(DA) (DT)(DT)(DG)(DC)(DT)(DT)(DT)(DA)(DA)(DA) (DG)(DG)(DC)(DA)(DG)(DA)(DG)(DG)(DA) (DC)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DA)(DT) (DC) (DA)(DG)(DT)(DC)(DC)(DA)(DA)(DA) (DC)(DT)(DT)(DC)(DT)(DT)(DT)(DC)(DT)(DG) (DC)(DA) (DT)(DG)(DT)(DA)(DC)(DA)(DT) (DG)(DG)(DA)(DA)(DA)(DA)(DC)(DT)(DG)(DG) (DC)(DC)(DA) (DA)(DG)(DG)(DC)(DA)(DA) (DA)(DC)(DA)(DC)(DG)(DT)(DC)(DC)(DG)(DG) (DA)(DA)(DT)(DG) (DA)(DT)(DG)(DG)(DT) (DA)(DT)(DT)(DT)(DA)(DA)(DG)(DA)(DA)(DC) (DA)(DA)(DA)(DC)(DA) (DT)(DT)(DC)(DC) (DC)(DT)(DG)(DG)(DT)(DA)(DT)(DC)(DA)(DG) (DC)(DA)(DA)(DG)(DT)(DA) (DC)(DA)(DG) (DT)(DG)(DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG) (DA)(DC)(DA)(DG)(DA)(DG)(DC) (DA)(DG) (DG)(DA)(DG)(DA)(DC)(DA)(DC)(DA)(DA)(DA) (DG)(DT)(DA)(DC)(DC)(DA)(DT)(DC) (DT) (DC)(DG)(DG)(DA)(DT)

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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 (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 #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 (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.165551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKTRSS RAGLQFPVGR VHRLLRKGNY SERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #6: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.935239 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: Maltose/maltodextrin-binding periplasmic protein,Transcription fa...

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,Transcription factor GATA-4
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.880258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH GSSMKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS A LMFNLQEP ...String:
MGSSHHHHHH GSSMKIEEGK LVIWINGDKG YNGLAEVGKK FEKDTGIKVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGL LAEITPDKAF QDKLYPFTWD AVRYNGKLIA YPIAVEALSL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS A LMFNLQEP YFTWPLIAAD GGYAFKYENG KYDIKDVGVD NAGAKAGLTF LVDLIKNKHM NADTDYSIAE AAFNKGETAM TI NGPWAWS NIDTSKVNYG VTVLPTFKGQ PSKPFVGVLS AGINAASPNK ELAKEFLENY LLTDEGLEAV NKDKPLGAVA LKS YEEELA KDPRIAATME NAQKGEIMPN IPQMSAFWYA VRTAVINAAS GRQTVDEALK DAQTNGIEEN LYFQSNAMYQ SLAM AANHG PPPGAYEAGG PGAFMHGAGA ASSPVYVPTP RVPSSVLGLS YLQGGGAGSA SGGASGGSSG GAASGAGPGT QQGSP GWSQ AGADGAAYTP PPVSPRFSFP GTTGSLAAAA AAAAAREAAA YSSGGGAAGA GLAGREQYGR AGFAGSYSSP YPAYMA DVG ASWAAAAAAS AGPFDSPVLH SLPGRANPAA RHPNLDMFDD FSEGRECVNC GAMSTPLWRR DGTGHYLCNA CGLYHKM NG INRPLIKPQR RLSASRRVGL SCANCQTTTT TLWRRNAEGE PVCNACGLYM KLHGVPRPLA MRKEGIQTRK RKPKNLNK S KTPAAPSGSE SLPPASGASS NSSNATTSSS EEMRPIKTEP GLSSHYGHSS SVSQTFSVSA MSGHGPSIHP VLSALKLSP QGYASPVSQS PQTSSKQDSW NSLVLADSHG DIITA

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, Transcription factor GATA-4

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1) / Number images used: 97849
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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