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- EMDB-6981: RNA polymerase II elongation complex stalled at SHL(-6) of the nu... -

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Basic information

Entry
Database: EMDB / ID: EMD-6981
TitleRNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome
Map data
SampleRNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome
  • (DNA-directed RNA polymerase ...Polymerase) x 3
  • (RNA polymerase II ...) x 4
  • (RNA polymerase subunit ...) x 4
  • DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
  • (nucleic-acidNucleic acid) x 3
  • Histone H3.3H3F3A
  • Histone H4
  • Histone H2A type 1-B/E
  • Histone H2B type 1-J
  • (ligand) x 2
Function / homology
Function and homology information


telomeric repeat-containing RNA transcription by RNA polymerase II / regulation of septum digestion after cytokinesis / heterochromatin assembly by small RNA / RNA polymerase III activity / nucleosomal DNA binding / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / termination of RNA polymerase II transcription / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA polymerase II activity ...telomeric repeat-containing RNA transcription by RNA polymerase II / regulation of septum digestion after cytokinesis / heterochromatin assembly by small RNA / RNA polymerase III activity / nucleosomal DNA binding / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / termination of RNA polymerase II transcription / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA polymerase II activity / RNA polymerase I activity / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of translational initiation / negative regulation of megakaryocyte differentiation / tRNA transcription by RNA polymerase III / Packaging Of Telomere Ends / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected purine / Deposition of new CENPA-containing nucleosomes at the centromere / transcription by RNA polymerase I / DNA replication-independent chromatin assembly / transcription by RNA polymerase III / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / RNA polymerase II, core complex / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Inhibition of DNA recombination at telomere / RNA polymerase II core promoter sequence-specific DNA binding / Meiotic synapsis / pericentric heterochromatin / heterochromatin assembly => GO:0031507 / telomere organization / transcription initiation from RNA polymerase II promoter / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / translation initiation factor binding / DNA replication-dependent chromatin assembly / DNA methylation / innate immune response in mucosa / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Condensation of Prophase Chromosomes / PRC2 methylates histones and DNA / Defective pyroptosis / RNA Polymerase I Promoter Escape / HDACs deacetylate histones / nuclear chromosome / Transcriptional regulation by small RNAs / NoRC negatively regulates rRNA expression / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / B-WICH complex positively regulates rRNA expression / DNA-templated transcription, initiation / ribonucleoside binding / Metalloprotease DUBs / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / lipopolysaccharide binding / DNA Damage/Telomere Stress Induced Senescence / G2/M DNA damage checkpoint / RMTs methylate histone arginines / nucleosome assembly / DNA-directed 5'-3' RNA polymerase activity / transcription by RNA polymerase II / DNA-directed RNA polymerase / HCMV Early Events / HDMs demethylate histones / Pre-NOTCH Transcription and Translation / Meiotic recombination / PKMTs methylate histone lysines / nucleosome / Activation of anterior HOX genes in hindbrain development during early embryogenesis / UCH proteinases / Transcriptional regulation of granulopoiesis / single-stranded DNA binding / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / single-stranded RNA binding / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / Senescence-Associated Secretory Phenotype (SASP) / chromosome, telomeric region / killing of cells of another organism / positive regulation of cell growth / Oxidative Stress Induced Senescence / antibacterial humoral response / Estrogen-dependent gene expression / nucleic acid binding / antimicrobial humoral immune response mediated by antimicrobial peptide / Ub-specific processing proteases / defense response to Gram-negative bacterium / RNA-directed 5'-3' RNA polymerase activity / defense response to Gram-positive bacterium / protein heterodimerization activity
Similarity search - Function
Rpb4/RPC9 superfamily / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1 C-terminal repeat ...Rpb4/RPC9 superfamily / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases N / 8 kDa subunit / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, Rpb5, N-terminal / RNA polymerase subunit 8 / RNA polymerase Rpb8 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / : / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / : / RNA polymerase Rpb5, C-terminal domain / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases K / 14 to 18 Kd subunits signature. / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / Transcription factor S-II (TFIIS) / Zinc finger, TFIIS-type / C2C2 Zinc finger / Zinc finger TFIIS-type profile. / S1 RNA binding domain / Histone H2B signature. / Histone H2B / Histone H2B / S1 domain / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone H2A / Histone 2A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / 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 H3 signature 1. / RNA polymerase Rpb1, domain 3 superfamily / Histone H3 signature 2. / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / Histone H3 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / Histone H3/CENP-A / RNA polymerase Rpb2, domain 2 superfamily / : / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit beta / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II subunit ...DNA-directed RNA polymerase subunit beta / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / RNA polymerase II third largest subunit B44, part of central core / RNA polymerase II subunit / RNA polymerase subunit ABC10-alpha / DNA-directed RNA polymerase subunit / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / Histone H3.3
Similarity search - Component
Biological speciesKomagataella phaffii (fungus) / Yeast (fungus) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 Å
AuthorsKujirai T / Ehara H / Fujino Y / Shirouzu M / Sekine S / Kurumizaka H
Funding support Japan, 6 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP25116002 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101076 Japan
Japan Society for the Promotion of ScienceJP15H04344 Japan
Japan Science and TechnologyJPMJCR16G1 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101082 Japan
RIKEN Dynamic Structural Biology project Japan
CitationJournal: Science / Year: 2018
Title: Structural basis of the nucleosome transition during RNA polymerase II passage.
Authors: Tomoya Kujirai / Haruhiko Ehara / Yuka Fujino / Mikako Shirouzu / Shun-Ichi Sekine / Hitoshi Kurumizaka /
Abstract: Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo- ...Genomic DNA forms chromatin, in which the nucleosome is the repeating unit. The mechanism by which RNA polymerase II (RNAPII) transcribes the nucleosomal DNA remains unclear. Here we report the cryo-electron microscopy structures of RNAPII-nucleosome complexes in which RNAPII pauses at the superhelical locations SHL(-6), SHL(-5), SHL(-2), and SHL(-1) of the nucleosome. RNAPII pauses at the major histone-DNA contact sites, and the nucleosome interactions with the RNAPII subunits stabilize the pause. These structures reveal snapshots of nucleosomal transcription, in which RNAPII gradually tears DNA from the histone surface while preserving the histone octamer. The nucleosomes in the SHL(-1) complexes are bound to a "foreign" DNA segment, which might explain the histone transfer mechanism. These results provide the foundations for understanding chromatin transcription and epigenetic regulation.
History
DepositionJun 25, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
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: 0.038
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.038
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6a5o
  • Surface level: 0.038
  • 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_6981.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.)
1.49 Å/pix.
x 240 pix.
= 357.6 Å
1.49 Å/pix.
x 240 pix.
= 357.6 Å
1.49 Å/pix.
x 240 pix.
= 357.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.49 Å
Density
Contour LevelBy AUTHOR: 0.038 / Movie #1: 0.038
Minimum - Maximum-0.025681142 - 0.13163014
Average (Standard dev.)0.0010234157 (±0.0070072715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 357.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.491.491.49
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z357.600357.600357.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0260.1320.001

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Supplemental data

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Additional map: nucleosome, postprocessed

Fileemd_6981_additional.map
Annotationnucleosome, postprocessed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire RNA polymerase II elongation complex stalled at SHL(-6) of the nu...

EntireName: RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome
Number of Components: 22

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Component #1: protein, RNA polymerase II elongation complex stalled at SHL(-6) ...

ProteinName: RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome
Recombinant expression: No
SourceSpecies: Komagataella phaffii (fungus) / Strain: GS115

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Component #2: protein, DNA-directed RNA polymerase subunit

ProteinName: DNA-directed RNA polymerase subunitPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 194.107422 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #3: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 139.746094 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #4: protein, RNA polymerase II third largest subunit B44, part of cen...

ProteinName: RNA polymerase II third largest subunit B44, part of central core
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.216293 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #5: protein, RNA polymerase II subunit B32

ProteinName: RNA polymerase II subunit B32 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.62298 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #6: protein, RNA polymerase subunit ABC27, common to RNA polymerases ...

ProteinName: RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.96268 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #7: protein, RNA polymerase subunit ABC23, common to RNA polymerases ...

ProteinName: RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.803588 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #8: protein, RNA polymerase II subunit

ProteinName: RNA polymerase II subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 18.802625 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.24922 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #10: protein, DNA-directed RNA polymerase subunit

ProteinName: DNA-directed RNA polymerase subunitPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.61232 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #11: protein, RNA polymerase subunit ABC10-beta, common to RNA polymer...

ProteinName: RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.554064 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #12: protein, RNA polymerase II subunit B12.5

ProteinName: RNA polymerase II subunit B12.5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.832896 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #13: protein, RNA polymerase subunit ABC10-alpha

ProteinName: RNA polymerase subunit ABC10-alpha / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.862048 kDa
SourceSpecies: Yeast (fungus) / Strain: GS115 / ATCC 20864

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Component #14: nucleic-acid, RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3')

nucleic acidName: RNA (5'-R(P*UP*GP*GP*GP*UP*GP*GP*UP*GP*GP*C)-3') / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UUGGUGUGUU U
MassTheoretical: 3.479026 kDa
SourceSpecies: synthetic construct (others)

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Component #15: nucleic-acid, DNA (198-MER)

nucleic acidName: DNA (198-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(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:
(DA)(DT)(DC)(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)(DA)(DC)(DC)(DC) (DA)(DA)(DG)(DA)(DC)(DA)(DC)(DC)(DA)(DG) (DG)(DC)(DA)(DC)(DG)(DA)(DG)(DA)(DC)(DA) (DG)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DC)(DA) (DA)(DC)(DG)(DA)(DA)(DA)(DA)(DC)(DG)(DG) (DC)(DC)(DA)(DC)(DC)(DA)(DC)(DC)(DC)(DA) (DA)(DA)(DC)(DA)(DC)(DA)(DC)(DC)(DA)(DA) (DA)(DC)(DA)(DC)(DA)(DA)(DG)(DA)(DG)(DC) (DT)(DA)(DA)(DT)(DT)(DG)(DA)(DC)(DT)(DG) (DA)(DC)(DG)(DT)(DA)(DA)(DG)(DC)
MassTheoretical: 60.869977 kDa
SourceSpecies: synthetic construct (others)

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Component #16: nucleic-acid, DNA (198-MER)

nucleic acidName: DNA (198-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DG)(DC)(DT)(DT)(DA)(DC)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DT)(DG)(DG)(DC)(DC)(DA)(DT) (DC)(DT)(DT)(DT)(DG)(DT)(DG)(DT)(DT)(DT) (DG)(DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG) (DG)(DG)(DT)(DG)(DG)(DT) ...Sequence:
(DG)(DC)(DT)(DT)(DA)(DC)(DG)(DT)(DC)(DA) (DG)(DT)(DC)(DT)(DG)(DG)(DC)(DC)(DA)(DT) (DC)(DT)(DT)(DT)(DG)(DT)(DG)(DT)(DT)(DT) (DG)(DG)(DT)(DG)(DT)(DG)(DT)(DT)(DT)(DG) (DG)(DG)(DT)(DG)(DG)(DT)(DG)(DG)(DC)(DC) (DG)(DT)(DT)(DT)(DT)(DC)(DG)(DT)(DT)(DG) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG) (DT)(DC)(DT)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DT)(DG)(DT)(DC)(DT)(DT)(DG)(DG) (DG)(DT)(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)(DG)(DA)(DT)
MassTheoretical: 61.381906 kDa
SourceSpecies: synthetic construct (others)

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Component #17: protein, Histone H3.3

ProteinName: Histone H3.3H3F3A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.643262 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #18: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.676703 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #19: protein, Histone H2A type 1-B/E

ProteinName: Histone H2A type 1-B/E / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.447825 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #20: protein, Histone H2B type 1-J

ProteinName: Histone H2B type 1-J / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.217516 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #21: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #22: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 200 kV / Electron Dose: 50 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 12692
3D reconstructionSoftware: RELION / Resolution: 9.9 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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