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

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Entry
Database: EMDB / ID: 6986
TitleRNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position)
Map datawhole, postprocessed
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 / homologyRNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Histone H4, conserved site / RNA polymerase, subunit H/Rpb5, conserved site ...RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / Histone H4, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Histone H2A, C-terminal domain / Histone H2A conserved site / 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 subunit/transcription factor S / DNA-directed RNA polymerase, insert domain / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb4/RPC9, core / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, conserved site / HRDC-like superfamily / Histone H2A/H2B/H3 / 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 / Histone-fold / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase Rpb1, domain 4 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb3/Rpb11 dimerisation domain / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Histone H2A signature. / Histone H4 signature. / Eukaryotic RNA polymerase II heptapeptide repeat. / Histone H3 signature 1. / Histone H2B signature. / RNA polymerases D / 30 to 40 Kd subunits signature. / Histone H3 signature 2. / RNA polymerase Rpb2, domain 2 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / S1 RNA binding domain / 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 / Core histone H2A/H2B/H3/H4 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb4 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb7, N-terminal
Function and homology information
SourceKomagataella phaffii (fungus) / Yeast (fungus) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 6.9 Å resolution
AuthorsKujirai T / Ehara H / Fujino Y / Shirouzu M / Sekine S / Kurumizaka H
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 ...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 ReportPDB-ID: 6a5v

SummaryFull reportAbout validation report
DateDeposition: Jun 25, 2018 / Header (metadata) release: Oct 3, 2018 / Map release: Oct 3, 2018 / Last update: Nov 14, 2018

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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-6a5v
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6986.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.49 Å/pix.
= 357.6 Å
240 pix
1.49 Å/pix.
= 357.6 Å
240 pix
1.49 Å/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 Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.052211598 - 0.1518552
Average (Standard dev.)0.00090830715 (0.008049498)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 357.6 Å
α=β=γ: 90.0 deg.

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
NX/NY/NZ
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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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)(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)(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: 5 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

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