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- EMDB-11220: Cryo-EM structure of the regulatory linker of ALC1 bound to the n... -

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Basic information

Entry
Database: EMDB / ID: EMD-11220
TitleCryo-EM structure of the regulatory linker of ALC1 bound to the nucleosome's acidic patch: nucleosome class.
Map data
SampleCrosslinked complex of ALC1 regulatory linker and the nucleosome
  • HistonesHistone
  • DNA
  • (Chromodomain-helicase-DNA-binding protein 1- ...) x 2
  • Histone H3
  • Histone H4
  • Histone H2A type 1
  • Histone H2B 1.1
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homology
Function and homology information


ATP-dependent chromatin remodeler activity => GO:0140658 / DNA-templated transcription, initiation / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / nucleosome / : / DNA helicase / DNA helicase activity / chromatin remodeling / protein heterodimerization activity ...ATP-dependent chromatin remodeler activity => GO:0140658 / DNA-templated transcription, initiation / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / nucleosome / : / DNA helicase / DNA helicase activity / chromatin remodeling / protein heterodimerization activity / DNA repair / cellular response to DNA damage stimulus / nucleotide binding / DNA binding / nucleoplasm / ATP binding / plasma membrane / nucleus / cytosol
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 1-like / SNF2-like, N-terminal domain superfamily / SNF2-related domain / SNF2, N-terminal / DEAH-box subfamily ATP-dependent helicases signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. ...Chromodomain-helicase-DNA-binding protein 1-like / SNF2-like, N-terminal domain superfamily / SNF2-related domain / SNF2, N-terminal / DEAH-box subfamily ATP-dependent helicases signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A / Histone H2A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Helicase conserved C-terminal domain / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Histone-fold / Macro domain / Macro domain profile. / Macro domain-like / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Helicase, C-terminal / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H3 / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Chromodomain-helicase-DNA-binding protein 1-like
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / synthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsBacic L / Gaullier G / Croll TI / Deindl S
Funding support Sweden, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)ChromatinRemodeling Sweden
Citation
Journal: Protein Sci / Year: 2018
Title: UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Authors: Thomas D Goddard / Conrad C Huang / Elaine C Meng / Eric F Pettersen / Gregory S Couch / John H Morris / Thomas E Ferrin /
Abstract: UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and ...UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Authors: Croll TI
#3: Journal: IUCrJ / Year: 2020
Title: Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in
Authors: Zivanov J / Nakane T / Scheres SHW
#4: Journal: J. Struct. Biol. / Year: 2012
Title: RELION: implementation of a Bayesian approach to cryo-EM structure determination.
Authors: Scheres SH
History
DepositionJun 24, 2020-
Header (metadata) releaseDec 23, 2020-
Map releaseDec 23, 2020-
UpdateJul 14, 2021-
Current statusJul 14, 2021Processing site: PDBe / 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 cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6zhx
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11220.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 196.2 Å
0.65 Å/pix.
x 300 pix.
= 196.2 Å
0.65 Å/pix.
x 300 pix.
= 196.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.654 Å
Density
Contour LevelBy AUTHOR: 0.0075 / Movie #1: 0.015
Minimum - Maximum-0.03190081 - 0.09921701
Average (Standard dev.)0.00013733856 (±0.0035894632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 196.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6540.6540.654
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z196.200196.200196.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0320.0990.000

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Supplemental data

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Segmentation: #1

Fileemd_11220_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Map from final 3D refinement in RELION.

Fileemd_11220_additional_1.map
AnnotationMap from final 3D refinement in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Sharpened map from RELION Post Process.

Fileemd_11220_additional_2.map
AnnotationSharpened map from RELION PostProcess.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Sharpened map from RELION Post Process, with masking.

Fileemd_11220_additional_3.map
AnnotationSharpened map from RELION PostProcess, with masking.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half-map 2 from final 3D refinement in RELION.

Fileemd_11220_half_map_1.map
AnnotationHalf-map 2 from final 3D refinement in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half-map 1 from final 3D refinement in RELION.

Fileemd_11220_half_map_2.map
AnnotationHalf-map 1 from final 3D refinement in RELION.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Crosslinked complex of ALC1 regulatory linker and the nucleosome

EntireName: Crosslinked complex of ALC1 regulatory linker and the nucleosome
Number of Components: 12

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Component #1: protein, Crosslinked complex of ALC1 regulatory linker and the nu...

ProteinName: Crosslinked complex of ALC1 regulatory linker and the nucleosome
Recombinant expression: No
MassTheoretical: 206.653 kDa

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Component #2: protein, Histones

ProteinName: HistonesHistone / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, DNA

ProteinName: DNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Chromodomain-helicase-DNA-binding protein 1-like

ProteinName: Chromodomain-helicase-DNA-binding protein 1-like / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: synthetic construct (others)

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Component #5: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.403062 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Histone H2A type 1

ProteinName: Histone H2A type 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.109436 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.655948 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: nucleic-acid, DNA (145-MER) Widom 601 sequence

nucleic acidName: DNA (145-MER) Widom 601 sequence / 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)(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)(DG)(DA)(DT)
MassTheoretical: 44.520383 kDa
SourceSpecies: synthetic construct (others)

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Component #10: nucleic-acid, DNA (145-MER) Widom 601 sequence

nucleic acidName: DNA (145-MER) Widom 601 sequence / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DT)(DC)(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:
(DA)(DT)(DC)(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)(DG)(DA)(DT)
MassTheoretical: 44.99166 kDa
SourceSpecies: synthetic construct (others)

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Component #11: protein, Chromodomain-helicase-DNA-binding protein 1-like

ProteinName: Chromodomain-helicase-DNA-binding protein 1-like / Details: Synthetic peptide biotinylated at its C-terminus. / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 4.073678 kDa
SourceSpecies: Homo sapiens (human)

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Component #12: ligand, water

LigandName: water / Number of Copies: 146 / Recombinant expression: No
MassTheoretical: 1.801505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.32 mg/mL / pH: 7.5
Support filmcurrent 20 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: Blot time 2.5 s, blot force 0. Two sample applications and blots were performed before vitrification..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: TFS KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 50.4 e/Å2 / Illumination Mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Energy Filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: OTHER

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Image acquisition

Image acquisitionNumber of Digital Images: 19897

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Image processing

ProcessingMethod: single particle reconstruction / Applied Symmetry: C1 (asymmetric) / Number of Projections: 636544
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 2.5 Å / Resolution Method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target Criteria: Real-space CC between model and map / Refinement space: REAL
Input PDB model: 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 3LZ0, 1ZLA
Chain ID: A, B, C, D, E, F, G, H, I, J, K
Output model

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