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- EMDB-9999: Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) -

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Basic information

Entry
Database: EMDB / ID: EMD-9999
TitleCryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom)
Map data
SampleHuman MLL1 complex associated with an H2B-monoubiquitinated nucleosome (4.0 angstrom)
  • Human MLL1 complexKMT2A
  • 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
  • Ubiquitin
  • Set1/Ash2 histone methyltransferase complex subunit ASH2
  • WD repeat-containing protein 5
  • (ligand) x 2
Function / homology
Function and homology information


euchromatin binding / positive regulation of cellular response to drug / regulation of histone H3-K14 acetylation / 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 / positive regulation of cellular response to drug / regulation of histone H3-K14 acetylation / 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 / minor groove of adenine-thymine-rich DNA binding / regulation of histone H3-K9 acetylation / Set1C/COMPASS complex / MLL3/4 complex / histone H4-K5 acetylation / histone H4-K8 acetylation / Ada2/Gcn5/Ada3 transcription activator complex / histone H3-K4 methylation / histone H4-K16 acetylation / embryonic hemopoiesis / negative regulation of histone H3-K4 methylation / MLL1 complex / beta-catenin-TCF complex assembly / positive regulation of gluconeogenesis / positive regulation of histone H3-K4 methylation / nuclear euchromatin / hemopoiesis / SRP-dependent cotranslational protein targeting to membrane / regulation of hematopoietic stem cell differentiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / histone acetyltransferase complex / viral transcription / histone H3 acetylation / translational initiation / MyD88-independent toll-like receptor signaling pathway / nucleotide-binding oligomerization domain containing signaling pathway / nucleotide-excision repair, DNA gap filling / nucleotide-excision repair, DNA damage recognition / histone methyltransferase complex / DNA-templated transcription, initiation / nucleotide-excision repair, DNA duplex unwinding / TRIF-dependent toll-like receptor signaling pathway / global genome nucleotide-excision repair / methylated histone binding / host cell / nucleotide-excision repair, preincision complex assembly / endosomal transport / intracellular transport of virus / MyD88-dependent toll-like receptor signaling pathway / DNA damage response, detection of DNA damage / nucleotide-excision repair, DNA incision, 5'-to lesion / regulation of megakaryocyte differentiation / 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 / protein tag / interstrand cross-link repair / endocytic vesicle membrane / error-prone translesion synthesis / stress-activated MAPK cascade / interleukin-1-mediated signaling pathway / regulation of transcription from RNA polymerase II promoter in response to hypoxia / I-kappaB kinase/NF-kappaB signaling / transcription-coupled nucleotide-excision repair / viral life cycle / negative regulation of transforming growth factor beta receptor signaling pathway / neuron projection development / beta-catenin binding / translesion synthesis / cytosolic small ribosomal subunit / transcription by RNA polymerase II / transforming growth factor beta receptor signaling pathway / virion assembly / anaphase-promoting complex-dependent catabolic process / transmembrane transport / small ribosomal subunit / regulation of mRNA stability / protein-containing complex assembly / membrane organization / post-translational protein modification / protein polyubiquitination / histone binding / go:0044212: / Wnt signaling pathway / mitochondrial outer membrane / vesicle / structural constituent of ribosome / activation of MAPK activity / response to estrogen / endosome membrane / positive regulation of NF-kappaB transcription factor activity / protein ubiquitination / translation
Ubiquitin-like domain / TATA box binding protein associated factor (TAF) / Ubiquitin conserved site / Histone H4, conserved site / Zinc finger, PHD-finger / WD40 repeat, conserved site / WD40-repeat-containing domain / Methyltransferase, trithorax / WD40/YVTN repeat-like-containing domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily ...Ubiquitin-like domain / TATA box binding protein associated factor (TAF) / Ubiquitin conserved site / Histone H4, conserved site / Zinc finger, PHD-finger / WD40 repeat, conserved site / WD40-repeat-containing domain / Methyltransferase, trithorax / WD40/YVTN repeat-like-containing domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Zinc finger, RING/FYVE/PHD-type / Zinc-binding ribosomal protein / SET domain / Histone-fold / Histone H2A/H2B/H3 / FY-rich, C-terminal / G-protein beta WD-40 repeat / FY-rich, N-terminal / SPRY domain / Post-SET domain / Ribosomal protein S27a / Zinc finger, CXXC-type / Histone H2A / Zinc finger, PHD-type / Histone H4 / B30.2/SPRY domain / WD40 repeat / Bromodomain / Histone H3/CENP-A / Histone H2B / Ubiquitin domain / Zinc finger, FYVE/PHD-type / Ubiquitin-like domain superfamily / Histone H2A conserved site / KMT2A, PHD domain 2 / KMT2A, PHD domain 1 / KMT2A, ePHD domain / Histone-lysine N-methyltransferase 2A / WD40-repeat-containing protein Swd3/WDR5 / Retinoblastoma-binding protein 5/Swd1 / Histone methyltransferase complex subunit ASH2 / Bromodomain-like superfamily / WD40-repeat-containing domain superfamily / CENP-T/Histone H4, histone fold / Extended PHD (ePHD) domain / S27a-like superfamily / Histone H2A, C-terminal domain
Histone H3.2 / Histone H2A / Retinoblastoma-binding protein 5 / Histone-lysine N-methyltransferase 2A / Histone H2B 1.1 / Ubiquitin-40S ribosomal protein S27a / Histone H4 / WD repeat-containing protein 5 / Histone H2A type 1 / Histone H3 / 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: 4 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: 6kiv

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-6kiv
  • 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_9999.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: 0.011 / Movie #1: 0.015
Minimum - Maximum-0.20788386 - 0.3480923
Average (Standard dev.)-0.00037078225 (±0.011542585)
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-0.0690.107-0.000

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Supplemental data

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Segmentation: #1

Fileemd_9999_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: additional map shows the major binding mode of H2BK120ub1 to RBBP5

Fileemd_9999_additional_1.map
Annotationadditional map shows the major binding mode of H2BK120ub1 to RBBP5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: additional map shows the minor binding mode 1 of H2BK120ub1 to RBBP5

Fileemd_9999_additional_2.map
Annotationadditional map shows the minor binding mode 1 of H2BK120ub1 to RBBP5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: additional map shows the minor binding mode 2 of H2BK120ub1 to RBBP5

Fileemd_9999_additional_3.map
Annotationadditional map shows the minor binding mode 2 of H2BK120ub1 to RBBP5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: additional map shows EM densities of ASH2L Pre-SPRY domain

Fileemd_9999_additional_4.map
Annotationadditional map shows EM densities of ASH2L Pre-SPRY domain
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 (4.0 angstrom)
Number of components: 16

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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 (4.0 angstrom)
Recombinant expression: No

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Component #2: protein, Human MLL1 complex

ProteinName: Human MLL1 complexKMT2A / 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, 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 #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, 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 #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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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 127898
3D reconstructionResolution: 4 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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