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- EMDB-10156: Class 2B : CENP-A nucleosome in complex with CENP-C central region -

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Basic information

Entry
Database: EMDB / ID: EMD-10156
TitleClass 2B : CENP-A nucleosome in complex with CENP-C central region
Map dataClass 2B : CENP-A nucleosome in complex with CENP-C central region
Sample
  • Complex: Class 2B : CENP-A nucleosome in complex with CENP-C central region
    • Other: CENP-A nucleosome
Function / homology
Function and homology information


spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing nucleosome / protein localization to chromosome, centromeric region / CENP-A containing chromatin assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / kinetochore assembly / establishment of mitotic spindle orientation / mitotic cytokinesis ...spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing nucleosome / protein localization to chromosome, centromeric region / CENP-A containing chromatin assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / kinetochore assembly / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / mitotic metaphase chromosome alignment / pericentric heterochromatin / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Packaging Of Telomere Ends / Mitotic Prometaphase / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / EML4 and NUDC in mitotic spindle formation / telomere organization / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Resolution of Sister Chromatid Cohesion / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / chromosome segregation / Transcriptional regulation by small RNAs / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / RHO GTPases Activate Formins / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / kinetochore / RMTs methylate histone arginines / Metalloprotease DUBs / innate immune response in mucosa / HCMV Early Events / structural constituent of chromatin / Separation of Sister Chromatids / nucleosome / Regulation of PD-L1(CD274) transcription / mitotic cell cycle / UCH proteinases / nucleosome assembly / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Dengue Virus-Host Interactions / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / antimicrobial humoral immune response mediated by antimicrobial peptide / heterochromatin formation / antibacterial humoral response / Oxidative Stress Induced Senescence / chromatin organization / Estrogen-dependent gene expression / nuclear body / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / protein heterodimerization activity / Amyloid fiber formation / cell division / chromatin binding / protein-containing complex / DNA binding
Similarity search - Function
CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / : ...CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
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
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsAli-Ahmad A / Bilokapic S / Halic M / Sekulic N
Funding support Norway, Germany, 2 items
OrganizationGrant numberCountry
Norwegian Research Council263195 Norway
European Research CouncilERC-smallRNAhet-309584 Germany
CitationJournal: EMBO Rep / Year: 2019
Title: CENP-C unwraps the human CENP-A nucleosome through the H2A C-terminal tail.
Authors: Ahmad Ali-Ahmad / Silvija Bilokapić / Ingmar B Schäfer / Mario Halić / Nikolina Sekulić /
Abstract: Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is ...Centromeres are defined epigenetically by nucleosomes containing the histone H3 variant CENP-A, upon which the constitutive centromere-associated network of proteins (CCAN) is built. CENP-C is considered to be a central organizer of the CCAN. We provide new molecular insights into the structure of human CENP-A nucleosomes, in isolation and in complex with the CENP-C central region (CENP-C ), the main CENP-A binding module of human CENP-C. We establish that the short αN helix of CENP-A promotes DNA flexibility at the nucleosome ends, independently of the sequence it wraps. Furthermore, we show that, in vitro, two regions of human CENP-C (CENP-C and CENP-C ) both bind exclusively to the CENP-A nucleosome. We find CENP-C to bind with high affinity due to an extended hydrophobic area made up of CENP-A and CENP-A . Importantly, we identify two key conformational changes within the CENP-A nucleosome upon CENP-C binding. First, the loose DNA wrapping of CENP-A nucleosomes is further exacerbated, through destabilization of the H2A C-terminal tail. Second, CENP-C rigidifies the N-terminal tail of H4 in the conformation favoring H4 monomethylation, essential for a functional centromere.
History
DepositionJul 30, 2019-
Header (metadata) releaseAug 14, 2019-
Map releaseAug 14, 2019-
UpdateOct 16, 2019-
Current statusOct 16, 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10156.png

Downloads & links

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Map

FileDownload / File: emd_10156.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClass 2B : CENP-A nucleosome in complex with CENP-C central region
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.01936764 - 0.045744933
Average (Standard dev.)0.00023889012 (±0.0025881464)
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-0.0190.0460.000

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Supplemental data

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Sample components

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Entire : Class 2B : CENP-A nucleosome in complex with CENP-C central region

EntireName: Class 2B : CENP-A nucleosome in complex with CENP-C central region
Components
  • Complex: Class 2B : CENP-A nucleosome in complex with CENP-C central region
    • Other: CENP-A nucleosome

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Supramolecule #2: Class 2B : CENP-A nucleosome in complex with CENP-C central region

SupramoleculeName: Class 2B : CENP-A nucleosome in complex with CENP-C central region
type: complex / ID: 2 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: CENP-A nucleosome

MacromoleculeName: CENP-A nucleosome / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSR LAREICVKFT RGVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV T LFPKDVQL ARRIRGLEEG LG MSGRGKG GKGLGKGGAK RHRKVLRDNI ...String:
MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSR LAREICVKFT RGVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV T LFPKDVQL ARRIRGLEEG LG MSGRGKG GKGLGKGGAK RHRKVLRDNI QGITKPAIRR LARRGGVKRI SGLIYEETRG VLKVFLENVI RDAVTYTEHA KRKTVTAMDV VYALKRQGRT LYGFGG GPL GMSGRGKQGG KARAKAKSRS SRAGLQFPVG RVHRLLRKGN YAERVGAGAP VYMAAVLEYL TAEILELAGN AARDNKKTRI IPRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHHKAKG K MPEPAKSA PAPKKGSKKA VTKAQKKDGK KRKRSRKESY SVYVYKVLKQ VHPDTGISSK AMGIMNSFVN DIFERIAGEA SRLAHYNKRS TITSREIQTA VRLLLPGELA KHAVSEGTKA VTKYTSSK A TCAGAATCCC GGTGCCGAGG CCGCTCAATT GGTCGTAGAC AGCTCTAGCA CCGCTTAAAC GCACGTACGC GCTGTCCCCC GCGTTTTAAC CGCCAAGGGG ATTACTCCCT AGTCTCCAGG CACGTGTCAG ATATATACAT CGAT ATCGA TGTATATATC TGACACGTGC CTGGAGACTA GGGAGTAATC CCCTTGGCGG TTAAAACGCG GGGGACAGCG CGTACGTGCG TTTAAGCGGT GCTAGAGCTG TCTACGACCA ATTGAGCGGC CTCGGCACCG GGATTCTGAT
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

Concentration1.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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