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- EMDB-22696: antibody and nucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-22696
Titleantibody and nucleosome complex
Map dataantibody and nucleosome complex
Sample
  • Complex: scFv and nucleosome complex
    • Protein or peptide: Cse4
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.1
    • Protein or peptide: Histone H2B.1
    • DNA: DNA (136-MER)
    • DNA: DNA (136-MER)
    • Protein or peptide: scFv
Keywordsnucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / replication fork protection complex ...HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Oxidative Stress Induced Senescence / replication fork protection complex / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / Ub-specific processing proteases / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA repair / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus
Similarity search - Function
: / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A ...: / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H2B.1 / Histone H4 / Histone H2A.1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae (brewer's yeast) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRuifang G / Yawen B
CitationJournal: Nat Commun / Year: 2021
Title: Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation.
Authors: Ruifang Guan / Tengfei Lian / Bing-Rui Zhou / Emily He / Carl Wu / Martin Singleton / Yawen Bai /
Abstract: Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to ...Accurate chromosome segregation relies on the specific centromeric nucleosome-kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.
History
DepositionSep 22, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k78
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22696.png

Downloads & links

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Map

FileDownload / File: emd_22696.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationantibody and nucleosome complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å		1.06 Å/pix.
x 240 pix.
= 254.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.12601496 - 0.21744803
Average (Standard dev.)0.000008608004 (±0.0076245014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z254.400254.400254.400
α/β/γ90.00090.00090.000
start NX/NY/NZ15150
NX/NY/NZ9999114
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1260.2170.000

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Supplemental data

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Sample components

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Entire : scFv and nucleosome complex

EntireName: scFv and nucleosome complex
Components
  • Complex: scFv and nucleosome complex
    • Protein or peptide: Cse4
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A.1
    • Protein or peptide: Histone H2B.1
    • DNA: DNA (136-MER)
    • DNA: DNA (136-MER)
    • Protein or peptide: scFv

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Supramolecule #1: scFv and nucleosome complex

SupramoleculeName: scFv and nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Cse4

MacromoleculeName: Cse4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 15.791588 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPK KYTPSELALY EIRKYQRSTD LLISKIPFAR LVKEVTDEFT TKDQDLRWQ SMAIMALQEA SEAYLVGLLE HTNLLALHAK RITIMKKDMQ LARRIRGQFI

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 11.39539 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL IYEEVRAVLK SFLESVIRDS VTYTEHAKRK TVTSLDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A.1

MacromoleculeName: Histone H2A.1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.013177 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAI RNDDELNKLL GNVTIAQGGV LPNIHQNLLP KKSAKATKAS QEL

UniProtKB: Histone H2A.1

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Macromolecule #4: Histone H2B.1

MacromoleculeName: Histone H2B.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.280362 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString:
MSAKAEKKPA SKAPAEKKPA AKKTSTSTDG KKRSKARKET YSSYIYKVLK QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNK KSTISAREIQ TAVRLILPGE LAKHAVSEGT RAVTKYSSST QA

UniProtKB: Histone H2B.1

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Macromolecule #7: scFv

MacromoleculeName: scFv / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.030146 KDa
Recombinant expressionOrganism: Escherichia phage EcSzw-2 (virus)
SequenceString: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ...String:
MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ASLGERVTIT CKASQDIRSY LSWYQQKPWK SPKTLIYYAT SLADGVPSRF SGSGSGQDFS LTINNLESDD TA TYYCLQH GESPYTFGSG TKLEIKRA

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Macromolecule #5: DNA (136-MER)

MacromoleculeName: DNA (136-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 42.219285 KDa
SequenceString: (DT)(DC)(DG)(DG)(DG)(DT)(DC)(DA)(DC)(DA) (DT)(DG)(DA)(DT)(DG)(DA)(DT)(DA)(DT)(DT) (DT)(DG)(DA)(DT)(DT)(DT)(DT)(DA)(DT) (DT)(DA)(DT)(DA)(DT)(DT)(DT)(DT)(DT)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DG) ...String:
(DT)(DC)(DG)(DG)(DG)(DT)(DC)(DA)(DC)(DA) (DT)(DG)(DA)(DT)(DG)(DA)(DT)(DA)(DT)(DT) (DT)(DG)(DA)(DT)(DT)(DT)(DT)(DA)(DT) (DT)(DA)(DT)(DA)(DT)(DT)(DT)(DT)(DT)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DG)(DT)(DA) (DA)(DA)(DA)(DA)(DA)(DT)(DA)(DA)(DA)(DA) (DA)(DG) (DT)(DA)(DG)(DT)(DT)(DT)(DA) (DT)(DT)(DT)(DT)(DT)(DA)(DA)(DA)(DA)(DA) (DA)(DT)(DA) (DA)(DA)(DA)(DT)(DT)(DT) (DA)(DA)(DA)(DA)(DT)(DA)(DT)(DT)(DA)(DG) (DT)(DG)(DT)(DA) (DT)(DT)(DT)(DG)(DA) (DT)(DT)(DT)(DC)(DC)(DG)(DA)(DA)(DA)(DG) (DT)(DT)(DA)(DA)(DA) (DA)(DA)(DA)(DG) (DA)(DA)(DA)(DT)(DA)(DG)(DT)(DA)(DA)(DG) (DC)(DT)

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Macromolecule #6: DNA (136-MER)

MacromoleculeName: DNA (136-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 41.679848 KDa
SequenceString: (DA)(DG)(DC)(DT)(DT)(DA)(DC)(DT)(DA)(DT) (DT)(DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DT)(DT)(DT)(DC)(DG)(DG)(DA) (DA)(DA)(DT)(DC)(DA)(DA)(DA)(DT)(DA)(DC) (DA) (DC)(DT)(DA)(DA)(DT)(DA) ...String:
(DA)(DG)(DC)(DT)(DT)(DA)(DC)(DT)(DA)(DT) (DT)(DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DT)(DT)(DT)(DC)(DG)(DG)(DA) (DA)(DA)(DT)(DC)(DA)(DA)(DA)(DT)(DA)(DC) (DA) (DC)(DT)(DA)(DA)(DT)(DA)(DT)(DT) (DT)(DT)(DA)(DA)(DA)(DT)(DT)(DT)(DT)(DA) (DT)(DT) (DT)(DT)(DT)(DT)(DA)(DA)(DA) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA)(DC) (DT)(DT)(DT) (DT)(DT)(DA)(DT)(DT)(DT) (DT)(DT)(DT)(DA)(DC)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DA)(DA) (DA)(DA)(DA)(DT)(DA) (DT)(DA)(DA)(DT)(DA)(DA)(DA)(DA)(DT)(DC) (DA)(DA)(DA)(DT)(DA) (DT)(DC)(DA)(DT) (DC)(DA)(DT)(DG)(DT)(DG)(DA)(DC)(DC)(DC) (DG)(DA)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 143164
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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