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- EMDB-10154: Class2C : CENP-A nucleosome in complex with CENP-C central region -

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Basic information

Entry
Database: EMDB / ID: EMD-10154
TitleClass2C : CENP-A nucleosome in complex with CENP-C central region
Map data
SampleCENP-A nucleosome in complex with CENP-C central region:
nucleosome / DNA / Histone H3-like centromeric protein A / Histone H4 / Histone H2A type 2-A / Histone H2B type 1-C/E/F/G/I / (nucleic-acidNucleic acid) x 2 / Centromere protein C
Function / homology
Function and homology information


Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / Meiotic synapsis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Packaging Of Telomere Ends / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA ...Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Recognition and association of DNA glycosylase with site containing an affected purine / Meiotic synapsis / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Packaging Of Telomere Ends / Pre-NOTCH Transcription and Translation / Formation of the beta-catenin:TCF transactivating complex / PRC2 methylates histones and DNA / Condensation of Prophase Chromosomes / Oxidative Stress Induced Senescence / Resolution of Sister Chromatid Cohesion / Separation of Sister Chromatids / Senescence-Associated Secretory Phenotype (SASP) / Mitotic Prometaphase / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Nonhomologous End-Joining (NHEJ) / Processing of DNA double-strand break ends / Deposition of new CENPA-containing nucleosomes at the centromere / G2/M DNA damage checkpoint / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RNA Polymerase I Promoter Opening / RNA Polymerase I Promoter Escape / E3 ubiquitin ligases ubiquitinate target proteins / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Estrogen-dependent gene expression / Meiotic recombination / Amyloid fiber formation / RHO GTPases Activate Formins / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / DNA Damage/Telomere Stress Induced Senescence / Transcriptional regulation by small RNAs / DNA methylation / HDACs deacetylate histones / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / SUMOylation of chromatin organization proteins / NoRC negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / HDMs demethylate histones / HATs acetylate histones / attachment of spindle microtubules to kinetochore involved in homologous chromosome segregation / condensed chromosome inner kinetochore / centromeric DNA binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / nuclear pericentric heterochromatin / Flemming body / condensed nuclear chromosome kinetochore / negative regulation of megakaryocyte differentiation / condensed nuclear chromosome, centromeric region / CENP-A containing nucleosome assembly / establishment of mitotic spindle orientation / DNA replication-independent nucleosome assembly / cleavage furrow / telomere capping / chromosome, centromeric region / intercellular bridge / pericentric heterochromatin / mitotic cytokinesis / innate immune response in mucosa / telomere organization / DNA replication-dependent nucleosome assembly / nuclear nucleosome / chromatin silencing at rDNA / negative regulation of gene expression, epigenetic / nucleosomal DNA binding / kinetochore / regulation of gene silencing by miRNA / nuclear chromosome / DNA-templated transcription, initiation / chromosome segregation / regulation of megakaryocyte differentiation / nucleosome assembly / nucleosome / protein heterotetramerization / midbody / chromatin organization / mitotic cell cycle / double-strand break repair via nonhomologous end joining / nuclear body / antibacterial humoral response / nuclear chromosome, telomeric region / antimicrobial humoral immune response mediated by antimicrobial peptide / protein ubiquitination / defense response to Gram-positive bacterium / cell division / nuclear chromatin / protein domain specific binding / chromatin binding / viral process / cellular protein metabolic process
RmlC-like jelly roll fold / Histone H2B / Histone H3/CENP-A / Histone H2B signature. / Histone H3 signature 2. / Histone H2A / Histone H2A signature. / Histone H4 / TATA box binding protein associated factor (TAF) / Histone H2A, C-terminal domain ...RmlC-like jelly roll fold / Histone H2B / Histone H3/CENP-A / Histone H2B signature. / Histone H3 signature 2. / Histone H2A / Histone H2A signature. / Histone H4 / TATA box binding protein associated factor (TAF) / Histone H2A, C-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Centromere assembly component CENP-C middle DNMT3B-binding region / Centromere kinetochore component CENP-T histone fold / Mif2/CENP-C like / Core histone H2A/H2B/H3/H4 / CENP-T/Histone H4, histone fold / Histone H2A conserved site / CENP-C, middle DNMT3B-binding domain / Histone H2A/H2B/H3 / Centromere protein C/Mif2/cnp3 / Kinetochore assembly subunit CENP-C, N-terminal domain / Mif2/CENP-C cupin domain / Histone H4, conserved site / Histone H4 signature. / RmlC-like cupin domain superfamily / Histone-fold / C-terminus of histone H2A
Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Histone H2A type 2-A
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAli-Ahmad A / Bilokapic S / Schafer IB / Halic M / Sekulic N
Funding support Norway, Germany, 2 items
OrganizationGrant numberCountry
Norwegian Research Council263195 Norway
European Research CouncilERC-smallRNAhet-309584 Germany
CitationJournal: To Be Published
Title: CryoEM structure of human CENP-A nucleosome alone and in complex with central domain of human CENP-C
Authors: Ali-Ahmad A / Bilokapic S / Schafer IB / Halic M / Sekulic N
Validation ReportPDB-ID: 6sef

SummaryFull reportAbout validation report
History
DepositionJul 29, 2019-
Header (metadata) releaseAug 14, 2019-
Map releaseAug 14, 2019-
UpdateAug 14, 2019-
Current statusAug 14, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6sef
  • Surface level: 0.012
  • 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_10154.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 168 pix.
= 218.4 Å
1.3 Å/pix.
x 168 pix.
= 218.4 Å
1.3 Å/pix.
x 168 pix.
= 218.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.01933752 - 0.04695393
Average (Standard dev.)0.0003152463 (±0.0025066645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 218.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z218.400218.400218.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0190.0470.000

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Supplemental data

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Sample components

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Entire CENP-A nucleosome in complex with CENP-C central region

EntireName: CENP-A nucleosome in complex with CENP-C central region
Number of components: 10

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Component #1: protein, CENP-A nucleosome in complex with CENP-C central region

ProteinName: CENP-A nucleosome in complex with CENP-C central region
Recombinant expression: No

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Component #2: protein, nucleosome

ProteinName: nucleosome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
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, Histone H3-like centromeric protein A

ProteinName: Histone H3-like centromeric protein A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 16.02363 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H2A type 2-A

ProteinName: Histone H2A type 2-A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 14.125549 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Histone H2B type 1-C/E/F/G/I

ProteinName: Histone H2B type 1-C/E/F/G/I / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.937213 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-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)(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 #9: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / 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)(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 #10: protein, Centromere protein C

ProteinName: Centromere protein C / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.20475 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.2 mg/mL / pH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 100 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: 40000
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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