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- EMDB-9252: CENP-A nucleosome bound by two copies of CENP-C(CD) and two copie... -

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Basic information

Entry
Database: EMDB / ID: EMD-9252
TitleCENP-A nucleosome bound by two copies of CENP-C(CD) and two copies CENP-N(NT) with local refinement
Map dataCENP-A nucleosome bound by two copies of CENP-CCD and two copies CENP-NNT with local refinement, primary map
Sample
  • Organelle or cellular component: chromatin complex
Function / homology
Function and homology information


spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / inner kinetochore / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / protein localization to CENP-A containing chromatin ...spindle attachment to meiosis I kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / inner kinetochore / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / mitotic cytokinesis / chromosome, centromeric region / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / pericentric heterochromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / arachidonate metabolic process / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / Resolution of Sister Chromatid Cohesion / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / chromosome segregation / RNA Polymerase I Promoter Escape / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / heterochromatin formation / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / kinetochore / Activation of anterior HOX genes in hindbrain development during early embryogenesis / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / nucleosome / Senescence-Associated Secretory Phenotype (SASP) / RUNX1 regulates transcription of genes involved in differentiation of HSCs / mitotic cell cycle / HATs acetylate histones / midbody / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / nuclear body / Ub-specific processing proteases / protein heterodimerization activity / Amyloid fiber formation / cell division / negative regulation of cell population proliferation / chromatin binding / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol
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 / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like ...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 / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / RmlC-like cupin domain superfamily / Lipoxygenase, iron binding site / Lipoxygenases iron-binding region signature 1. / Lipoxygenase / Lipoxygenase, C-terminal / Lipoxigenase, C-terminal domain superfamily / Lipoxygenase / Lipoxygenase iron-binding catalytic domain profile. / 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 / RmlC-like jelly roll fold / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3-like centromeric protein A / Arachidonate 15-lipoxygenase / Centromere protein C / Histone H2B type 2-F / Histone H2A type 1-C / Centromere protein N
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAllu PK / Black BE
CitationJournal: Curr Biol / Year: 2019
Title: Structure of the Human Core Centromeric Nucleosome Complex.
Authors: Praveen Kumar Allu / Jennine M Dawicki-McKenna / Trevor Van Eeuwen / Moriya Slavin / Merav Braitbard / Chen Xu / Nir Kalisman / Kenji Murakami / Ben E Black /
Abstract: Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the ...Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the histone H3 variant, CENP-A, and its binding proteins, CENP-C (through its central domain; CD) and CENP-N (through its N-terminal domain; NT). CENP-C can engage nucleosomes through two domains: the CD and the CENP-C motif (CM). CENP-C is part of the CCNC by virtue of its high specificity for CENP-A nucleosomes and ability to stabilize CENP-A at the centromere. CENP-C is thought to engage a neighboring nucleosome, either one containing conventional H3 or CENP-A, and a crystal structure of a nucleosome complex containing two copies of CENP-C was reported. Recent structures containing a single copy of CENP-N bound to the CENP-A nucleosome in the absence of CENP-C were reported. Here, we find that one copy of CENP-N is lost for every two copies of CENP-C on centromeric chromatin just prior to kinetochore formation. We present the structures of symmetric and asymmetric forms of the CCNC that vary in CENP-N stoichiometry. Our structures explain how the central domain of CENP-C achieves its high specificity for CENP-A nucleosomes and how CENP-C and CENP-N sandwich the histone H4 tail. The natural centromeric DNA path in our structures corresponds to symmetric surfaces for CCNC assembly, deviating from what is observed in prior structures using artificial sequences. At mitosis, we propose that CCNC asymmetry accommodates its asymmetric connections at the chromosome/kinetochore interface. VIDEO ABSTRACT.
History
DepositionOct 23, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseJul 24, 2019-
UpdateSep 4, 2019-
Current statusSep 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • 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_9252.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCENP-A nucleosome bound by two copies of CENP-CCD and two copies CENP-NNT with local refinement, primary map
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.029542444 - 0.066137895
Average (Standard dev.)0.00040339422 (±0.0028411003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-2600
NX/NY/NZ264044
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0300.0660.000

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Supplemental data

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Additional map: CENP-A nucleosome bound by two copies of CENP-CCD...

Fileemd_9252_additional.map
AnnotationCENP-A nucleosome bound by two copies of CENP-CCD and two copies CENP-NNT with local refinement, additional map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : chromatin complex

EntireName: chromatin complex
Components
  • Organelle or cellular component: chromatin complex

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Supramolecule #1: chromatin complex

SupramoleculeName: chromatin complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#11
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 276 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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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: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Version: 1.06
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Version: 3 / Number images used: 54139
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Version: 2.1
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Version: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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