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- EMDB-6986: RNA polymerase II elongation complex stalled at SHL(-1) of the nu... -

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Basic information

Entry
Database: EMDB / ID: EMD-6986
TitleRNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Map data
SampleRNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
  • (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 5
  • Histone H3.3H3F3A
  • Histone H4
  • Histone H2A, Histone H2A type 1-B/E
  • Histone H2B, Histone H2B type 1-J
  • (ligand) x 2
Function / homology
Function and homology information


regulation of septum digestion after cytokinesis / telomeric repeat-containing RNA transcription by RNA polymerase II / RNA polymerase III activity / heterochromatin assembly by small RNA / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin assembly / subtelomeric heterochromatin assembly ...regulation of septum digestion after cytokinesis / telomeric repeat-containing RNA transcription by RNA polymerase II / RNA polymerase III activity / heterochromatin assembly by small RNA / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / muscle cell differentiation / pericentric heterochromatin assembly / subtelomeric heterochromatin assembly / pericentric heterochromatin => GO:0005721 / nucleus organization / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / nucleosomal DNA binding / RNA polymerase II activity / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / spermatid development / positive regulation of translational initiation / RNA polymerase I activity / tRNA transcription by RNA polymerase III / oogenesis / RNA polymerase I complex / negative regulation of megakaryocyte differentiation / mRNA cleavage / RNA polymerase III complex / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase II, core complex / RNA polymerase II core promoter sequence-specific DNA binding / CENP-A containing nucleosome assembly / termination of RNA polymerase II transcription / negative regulation of tumor necrosis factor-mediated signaling pathway / single fertilization / DNA replication-independent nucleosome assembly / telomere capping / translation initiation factor binding / chromatin silencing / telomere organization / DNA replication-dependent nucleosome assembly / nucleosome => GO:0000786 / innate immune response in mucosa / rDNA heterochromatin assembly / negative regulation of gene expression, epigenetic / embryo implantation / regulation of gene silencing by miRNA / osteoblast differentiation / nuclear chromosome / ribonucleoside binding / DNA-templated transcription, initiation / P-body / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / regulation of megakaryocyte differentiation / nucleosome assembly / nucleosome / lipopolysaccharide binding / transcription by RNA polymerase II / multicellular organism growth / single-stranded DNA binding / cell population proliferation / male gonad development / single-stranded RNA binding / double-strand break repair via nonhomologous end joining / chromatin organization / chromosome, telomeric region => GO:0000781 / positive regulation of cell growth / nucleic acid binding / killing of cells of other organism / transcription initiation from RNA polymerase II promoter / antibacterial humoral response / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / protein ubiquitination / RNA-directed 5'-3' RNA polymerase activity / defense response to Gram-negative bacterium / protein heterodimerization activity / transcription, DNA-templated / defense response to Gram-positive bacterium / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / chromatin => GO:0000785 / protein domain specific binding / nucleotide binding / cellular protein metabolic process / nucleolus / protein-containing complex / RNA binding / DNA binding / extracellular space / extracellular exosome / zinc ion binding / membrane / extracellular region / nucleoplasm / metal ion binding / nucleus / cytosol
RNA polymerase, beta subunit, conserved site / Histone-fold / DNA-directed RNA polymerase, subunit N/Rpb10 / Histone H3/CENP-A / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 ...RNA polymerase, beta subunit, conserved site / Histone-fold / DNA-directed RNA polymerase, subunit N/Rpb10 / Histone H3/CENP-A / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / HRDC-like superfamily / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Histone H2A/H2B/H3 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Histone H4, conserved site / Histone H2B / RNA polymerase, alpha subunit / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase Rpb4/RPC9, core / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase Rpb7-like , N-terminal / RNA polymerase subunit RPB4/RPC9 / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / TATA box binding protein associated factor (TAF) / S1 domain / Histone H2A / Histone H4 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5, conserved site / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase Rpb7-like, N-terminal domain superfamily / Histone H2A, C-terminal domain / Pol II subunit B9, C-terminal zinc ribbon / CENP-T/Histone H4, histone fold / RPB5-like RNA polymerase subunit superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase RBP11 / RNA polymerase Rpb1, funnel domain superfamily / Rpb4/RPC9 superfamily / RNA polymerase Rpb1, domain 7 superfamily / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Histone H2A conserved site / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10
RNA polymerase II third largest subunit B44, part of central core / Histone H4 / Histone H2B type 1-J / Histone H2A type 1-B/E / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / RNA polymerase II subunit / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...RNA polymerase II third largest subunit B44, part of central core / Histone H4 / Histone H2B type 1-J / Histone H2A type 1-B/E / DNA-directed RNA polymerase subunit / RNA polymerase subunit ABC10-alpha / RNA polymerase II subunit / RNA polymerase II subunit B12.5 / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase II subunit B32 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III / RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III / DNA-directed RNA polymerase subunit beta / Histone H3.3
Biological speciesKomagataella phaffii (fungus) / Yeast (fungus) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 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.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 25, 2018-
Header (metadata) releaseOct 3, 2018-
Map releaseOct 3, 2018-
UpdateFeb 12, 2020-
Current statusFeb 12, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6inq
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6986.png

Downloads & links

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Map

FileDownload / File: emd_6986.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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.052211598 - 0.1518552
Average (Standard dev.)0.00090830715 (±0.008049498)
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
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0520.1520.001

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Supplemental data

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Additional map: nucleosome, postprocessed

Fileemd_6986_additional.map
Annotationnucleosome, postprocessed
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire RNA polymerase II elongation complex stalled at SHL(-1) of the nu...

EntireName: RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Number of components: 24

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

ProteinName: RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Recombinant expression: No
SourceSpecies: Komagataella phaffii (fungus) / Strain: GS115 / ATCC 20864

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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*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3')

nucleic acidName: RNA (5'-R(P*GP*UP*GP*UP*CP*UP*UP*GP*GP*GP*U)-3') / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUGUCUUGGG U
MassTheoretical: 3.517082 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)
MassTheoretical: 38.379488 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, Histone H2A type 1-B/E

ProteinName: Histone H2A, 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, Histone H2B type 1-J

ProteinName: Histone H2B, 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: nucleic-acid, DNA (31-MER)

nucleic acidName: DNA (31-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(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)
MassTheoretical: 9.544222 kDa
SourceSpecies: synthetic construct (others)

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Component #22: nucleic-acid, DNA (31-MER)

nucleic acidName: DNA (31-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(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)
MassTheoretical: 9.52007 kDa
SourceSpecies: synthetic construct (others)

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Component #23: ligand, ZINC ION

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

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Component #24: 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: 28961
3D reconstructionSoftware: RELION / Resolution: 6.9 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

6inq

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