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- EMDB-9998: Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) -

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Entry
Database: EMDB / ID: EMD-9998
TitleCryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom)
Map data
SampleHuman MLL1 complex associated with an H2B-monoubiquitinated nucleosome (3.2 angstrom)
  • Human MLL1KMT2A
  • H2B-monoubiquitinated nucleosome
  • Histone H3
  • Histone H4
  • Histone H2A
  • Histone H2B 1.1
  • (nucleic-acidNucleic acid) x 2
  • Histone-lysine N-methyltransferase 2A
  • Retinoblastoma-binding protein 5
  • WD repeat-containing protein 5
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
  • Ubiquitin
  • (ligand) x 4
Function / homology
Function and homology information


euchromatin binding / regulation of histone H3-K14 acetylation / positive regulation of cellular response to drug / positive regulation of transporter activity / negative regulation of DNA methylation / histone H3-K4 dimethylation / histone H3-K4 monomethylation / unmethylated CpG binding / histone methyltransferase activity (H3-K4 specific) / [histone H3]-lysine4 N-trimethyltransferase ...euchromatin binding / regulation of histone H3-K14 acetylation / positive regulation of cellular response to drug / positive regulation of transporter activity / negative regulation of DNA methylation / histone H3-K4 dimethylation / histone H3-K4 monomethylation / unmethylated CpG binding / histone methyltransferase activity (H3-K4 specific) / [histone H3]-lysine4 N-trimethyltransferase / histone H3-K4 trimethylation / Set1C/COMPASS complex / regulation of histone H3-K9 acetylation / MLL3/4 complex / histone H4-K5 acetylation / histone H4-K8 acetylation / minor groove of adenine-thymine-rich DNA binding / Ada2/Gcn5/Ada3 transcription activator complex / histone H3-K4 methylation / histone H4-K16 acetylation / negative regulation of histone H3-K4 methylation / embryonic hemopoiesis / beta-catenin-TCF complex assembly / MLL1 complex / positive regulation of histone H3-K4 methylation / positive regulation of gluconeogenesis / nuclear euchromatin / SRP-dependent cotranslational protein targeting to membrane / hemopoiesis / regulation of hematopoietic stem cell differentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / viral transcription / histone acetyltransferase complex / translational initiation / histone H3 acetylation / MyD88-independent toll-like receptor signaling pathway / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / histone methyltransferase complex / nucleotide-excision repair, DNA damage recognition / DNA-templated transcription, initiation / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / methylated histone binding / global genome nucleotide-excision repair / host cell / nucleotide-excision repair, preincision complex assembly / regulation of megakaryocyte differentiation / intracellular transport of virus / MyD88-dependent toll-like receptor signaling pathway / nucleotide-excision repair, DNA incision, 5'-to lesion / DNA damage response, detection of DNA damage / endosomal transport / lysine-acetylated histone binding / error-free translesion synthesis / modification-dependent protein catabolic process / nucleotide-excision repair, DNA incision / skeletal system development / protein targeting to peroxisome / JNK cascade / nucleosome / circadian regulation of gene expression / interstrand cross-link repair / protein tag / endocytic vesicle membrane / error-prone translesion synthesis / stress-activated MAPK cascade / regulation of transcription from RNA polymerase II promoter in response to hypoxia / interleukin-1-mediated signaling pathway / transcription-coupled nucleotide-excision repair / I-kappaB kinase/NF-kappaB signaling / viral life cycle / beta-catenin binding / neuron projection development / negative regulation of transforming growth factor beta receptor signaling pathway / translesion synthesis / cytosolic small ribosomal subunit / virion assembly / transforming growth factor beta receptor signaling pathway / anaphase-promoting complex-dependent catabolic process / transmembrane transport / small ribosomal subunit / regulation of mRNA stability / membrane organization / protein-containing complex assembly / post-translational protein modification / protein polyubiquitination / histone binding / Wnt signaling pathway / mitochondrial outer membrane / vesicle / structural constituent of ribosome / activation of MAPK activity / response to estrogen / endosome membrane / transcription regulatory region sequence-specific DNA binding / positive regulation of NF-kappaB transcription factor activity / protein ubiquitination / translation / protein deubiquitination
WD40/YVTN repeat-like-containing domain superfamily / Zinc finger, PHD-finger / SET domain / Ubiquitin-like domain / Histone H2B / Histone H3/CENP-A / WD40-repeat-containing domain / WD40 repeat, conserved site / Histone H4, conserved site / WD40 repeat ...WD40/YVTN repeat-like-containing domain superfamily / Zinc finger, PHD-finger / SET domain / Ubiquitin-like domain / Histone H2B / Histone H3/CENP-A / WD40-repeat-containing domain / WD40 repeat, conserved site / Histone H4, conserved site / WD40 repeat / Ubiquitin conserved site / Ubiquitin domain / G-protein beta WD-40 repeat / Ubiquitin-like domain superfamily / Methyltransferase, trithorax / Histone H2A conserved site / Extended PHD (ePHD) domain / Bromodomain / B30.2/SPRY domain / WD40-repeat-containing domain superfamily / TATA box binding protein associated factor (TAF) / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Zinc-binding ribosomal protein / Zinc finger, FYVE/PHD-type / Histone-fold / Histone H2A/H2B/H3 / FY-rich, C-terminal / Histone H4 / FY-rich, N-terminal / SPRY domain / Post-SET domain / Ribosomal protein S27a / Zinc finger, CXXC-type / Histone H2A / Zinc finger, PHD-type / CENP-T/Histone H4, histone fold / Histone H2A, C-terminal domain / Histone methyltransferase complex subunit ASH2 / Bromodomain-like superfamily / KMT2A, PHD domain 2 / KMT2A, PHD domain 1 / KMT2A, ePHD domain / S27a-like superfamily / Histone-lysine N-methyltransferase 2A / WD40-repeat-containing protein Swd3/WDR5 / Retinoblastoma-binding protein 5/Swd1
Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / WD repeat-containing protein 5 / Histone H4 / Ubiquitin-40S ribosomal protein S27a / Histone H3.2 / Histone-lysine N-methyltransferase 2A / Retinoblastoma-binding protein 5 / Histone H2A / Set1/Ash2 histone methyltransferase complex subunit ASH2
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHuang J / Xue H / Yao T
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (China) China
CitationJournal: Nature / Year: 2019
Title: Structural basis of nucleosome recognition and modification by MLL methyltransferases.
Authors: Han Xue / Tonghui Yao / Mi Cao / Guanjun Zhu / Yan Li / Guiyong Yuan / Yong Chen / Ming Lei / Jing Huang /
Abstract: Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and ...Methyltransferases of the mixed-lineage leukaemia (MLL) family-which include MLL1, MLL2, MLL3, MLL4, SET1A and SET1B-implement methylation of histone H3 on lysine 4 (H3K4), and have critical and distinct roles in the regulation of transcription in haematopoiesis, adipogenesis and development. The C-terminal catalytic SET (Su(var.)3-9, enhancer of zeste and trithorax) domains of MLL proteins are associated with a common set of regulatory factors (WDR5, RBBP5, ASH2L and DPY30) to achieve specific activities. Current knowledge of the regulation of MLL activity is limited to the catalysis of histone H3 peptides, and how H3K4 methyl marks are deposited on nucleosomes is poorly understood. H3K4 methylation is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120ub1), a prevalent histone H2B mark that disrupts chromatin compaction and favours open chromatin structures, but the underlying mechanism remains unknown. Here we report cryo-electron microscopy structures of human MLL1 and MLL3 catalytic modules associated with nucleosome core particles that contain H2BK120ub1 or unmodified H2BK120. These structures demonstrate that the MLL1 and MLL3 complexes both make extensive contacts with the histone-fold and DNA regions of the nucleosome; this allows ease of access to the histone H3 tail, which is essential for the efficient methylation of H3K4. The H2B-conjugated ubiquitin binds directly to RBBP5, orienting the association between MLL1 or MLL3 and the nucleosome. The MLL1 and MLL3 complexes display different structural organizations at the interface between the WDR5, RBBP5 and MLL1 (or the corresponding MLL3) subunits, which accounts for the opposite roles of WDR5 in regulating the activity of the two enzymes. These findings transform our understanding of the structural basis for the regulation of MLL activity at the nucleosome level, and highlight the pivotal role of nucleosome regulation in histone-tail modification.
Validation ReportPDB-ID: 6kiu

SummaryFull reportAbout validation report
History
DepositionJul 20, 2019-
Header (metadata) releaseSep 11, 2019-
Map releaseSep 11, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kiu
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9998.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 270 pix.
= 294.3 Å
1.09 Å/pix.
x 270 pix.
= 294.3 Å
1.09 Å/pix.
x 270 pix.
= 294.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.015
Minimum - Maximum-0.09355743 - 0.16271995
Average (Standard dev.)-0.00001254022 (±0.004828479)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 294.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z270270270
origin x/y/z0.0000.0000.000
length x/y/z294.300294.300294.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS270270270
D min/max/mean-0.0940.163-0.000

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Supplemental data

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Segmentation: #1

Fileemd_9998_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional map showing good density of RBBP5 AS

Fileemd_9998_additional_1.map
AnnotationAdditional map showing good density of RBBP5_AS
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional map showing good density of MLL1 AS

Fileemd_9998_additional_2.map
AnnotationAdditional map showing good density of MLL1_AS
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional map showing good density of H2BK120ub1

Fileemd_9998_additional_3.map
AnnotationAdditional map showing good density of H2BK120ub1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Additional map showing good density of ASH2L SPRY

Fileemd_9998_additional_4.map
AnnotationAdditional map showing good density of ASH2L_SPRY
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Human MLL1 complex associated with an H2B-monoubiquitinated nucle...

EntireName: Human MLL1 complex associated with an H2B-monoubiquitinated nucleosome (3.2 angstrom)
Number of components: 18

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Component #1: protein, Human MLL1 complex associated with an H2B-monoubiquitina...

ProteinName: Human MLL1 complex associated with an H2B-monoubiquitinated nucleosome (3.2 angstrom)
Recombinant expression: No

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Component #2: protein, Human MLL1

ProteinName: Human MLL1KMT2A / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, H2B-monoubiquitinated nucleosome

ProteinName: H2B-monoubiquitinated nucleosome / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)

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Component #4: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.30393 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.263231 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H2A

ProteinName: Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.978241 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.498715 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DC)(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) ...Sequence:
(DT)(DC)(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)(DG)(DA)
MassTheoretical: 44.521367 kDa
SourceSpecies: synthetic construct (others)

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Component #9: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DT)(DC)(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) ...Sequence:
(DT)(DC)(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)(DG)(DA)
MassTheoretical: 44.992648 kDa
SourceSpecies: synthetic construct (others)

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Component #10: protein, Histone-lysine N-methyltransferase 2A

ProteinName: Histone-lysine N-methyltransferase 2A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.970539 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: protein, Retinoblastoma-binding protein 5

ProteinName: Retinoblastoma-binding protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 59.223477 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: protein, WD repeat-containing protein 5

ProteinName: WD repeat-containing protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.635438 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #13: protein, Set1/Ash2 histone methyltransferase complex subunit ASH2

ProteinName: Set1/Ash2 histone methyltransferase complex subunit ASH2
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.288758 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #14: protein, Ubiquitin

ProteinName: Ubiquitin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.622922 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #15: ligand, S-ADENOSYL-L-HOMOCYSTEINE

LigandName: S-ADENOSYL-L-HOMOCYSTEINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.384411 kDa

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Component #16: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #17: ligand, LYSINE

LigandName: LYSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.147195 kDa

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Component #18: ligand, GLUTAMINE

LigandName: GLUTAMINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.146144 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 139535
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Output model

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