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

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Basic information

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


Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / Translesion synthesis by REV1 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ISG15 antiviral mechanism / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Oncogene Induced Senescence / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation ...Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / Translesion synthesis by REV1 / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ISG15 antiviral mechanism / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Oncogene Induced Senescence / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Constitutive Signaling by NOTCH1 HD Domain Mutants / Stimuli-sensing channels / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Regulation of PLK1 Activity at G2/M Transition / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / Oxidative Stress Induced Senescence / Separation of Sister Chromatids / Selenocysteine synthesis / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Downregulation of SMAD2/3:SMAD4 transcriptional activity / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / NOTCH2 Activation and Transmission of Signal to the Nucleus / PKMTs methylate histone lysines / Activated NOTCH1 Transmits Signal to the Nucleus / TAK1 activates NFkB by phosphorylation and activation of IKKs complex / Degradation of DVL / Degradation of AXIN / Asymmetric localization of PCP proteins / AUF1 (hnRNP D0) binds and destabilizes mRNA / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / activated TAK1 mediates p38 MAPK activation / Circadian Clock / HATs acetylate histones / ABC-family proteins mediated transport / Myoclonic epilepsy of Lafora / Deactivation of the beta-catenin transactivating complex / Autodegradation of the E3 ubiquitin ligase COP1 / Glycogen synthesis / RMTs methylate histone arginines / Downregulation of TGF-beta receptor signaling / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Cyclin B / DDX58/IFIH1-mediated induction of interferon-alpha/beta / TICAM1, RIP1-mediated IKK complex recruitment / Budding and maturation of HIV virion / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Peptide chain elongation / L13a-mediated translational silencing of Ceruloplasmin expression / Downregulation of ERBB2:ERBB3 signaling / Spry regulation of FGF signaling / Downregulation of ERBB4 signaling / ER-Phagosome pathway / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Membrane binding and targetting of GAG proteins / Regulation of activated PAK-2p34 by proteasome mediated degradation / Degradation of beta-catenin by the destruction complex / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / NRIF signals cell death from the nucleus / Downstream TCR signaling / Formation of the beta-catenin:TCF transactivating complex / TCF dependent signaling in response to WNT / Viral mRNA Translation / Assembly Of The HIV Virion / SCF(Skp2)-mediated degradation of p27/p21 / EGFR downregulation / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / SRP-dependent cotranslational protein targeting to membrane / APC-Cdc20 mediated degradation of Nek2A / Pink/Parkin Mediated Mitophagy / Stabilization of p53 / Downregulation of ERBB2 signaling / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / The role of GTSE1 in G2/M progression after G2 checkpoint / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Ubiquitin-dependent degradation of Cyclin D / Eukaryotic Translation Termination / GTP hydrolysis and joining of the 60S ribosomal subunit / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Formation of a pool of free 40S subunits / Translation initiation complex formation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / G2/M Checkpoints / E3 ubiquitin ligases ubiquitinate target proteins / Cyclin D associated events in G1 / CDK-mediated phosphorylation and removal of Cdc6 / Orc1 removal from chromatin / CDT1 association with the CDC6:ORC:origin complex / Negative regulation of MET activity / Regulation of TP53 Activity through Methylation
Ubiquitin domain profile. / Histone H3 signature 2. / PHD-finger / SET domain / Ribosomal protein S27a / CXXC zinc finger domain / F/Y-rich N-terminus / F/Y rich C-terminus / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A ...Ubiquitin domain profile. / Histone H3 signature 2. / PHD-finger / SET domain / Ribosomal protein S27a / CXXC zinc finger domain / F/Y-rich N-terminus / F/Y rich C-terminus / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Ubiquitin domain signature. / Histone H3 signature 1. / Histone H2B signature. / Trp-Asp (WD) repeats signature. / Zinc finger PHD-type signature. / WD domain, G-beta repeat / Zinc finger CXXC-type profile. / Extended PHD (ePHD) domain profile. / FYR domain FYRC motif profile. / FYR domain FYRN motif profile. / Post-SET domain profile. / Bromodomain profile. / Trp-Asp (WD) repeats circular profile. / SET domain profile. / B30.2/SPRY domain profile. / Trp-Asp (WD) repeats profile. / Zinc finger PHD-type profile. / SPRY domain / Ubiquitin family / Concanavalin A-like lectin/glucanase domain superfamily / 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 / Zinc finger, RING/FYVE/PHD-type / Ubiquitin / Zinc-binding ribosomal protein / Zinc finger, FYVE/PHD-type / Histone-fold / Histone H2A/H2B/H3 / TATA box binding protein associated factor (TAF) / FY-rich, C-terminal / Ubiquitin conserved site / G-protein beta WD-40 repeat / Core histone H2A/H2B/H3/H4 / Retinoblastoma-binding protein 5/Swd1 / 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 / Histone methyltransferase complex subunit ASH2 / Ubiquitin-like domain superfamily / Bromodomain-like superfamily / WD40-repeat-containing domain superfamily / CENP-T/Histone H4, histone fold / Extended PHD (ePHD) domain / Histone H2A conserved site / Histone H2A, C-terminal domain / SPRY domain / FY-rich, N-terminal / Post-SET domain / Ribosomal protein S27a / Histone H2B / Histone H3/CENP-A / Ubiquitin domain / SET domain / Zinc finger, CXXC-type / Histone H2A / Zinc finger, PHD-type / Histone H4 / B30.2/SPRY domain / WD40 repeat / Bromodomain
Histone H3 / Histone H2B 1.1 / WD repeat-containing protein 5 / Histone H4 / Ubiquitin-40S ribosomal protein S27a / 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-
UpdateSep 18, 2019-
Current statusSep 18, 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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Mask #1

Fileemd_9998_msk_1.map
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)(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)(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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