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- EMDB-14334: Structure of the human CCAN CENP-A alpha-satellite complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14334
TitleStructure of the human CCAN CENP-A alpha-satellite complex
Map data
Sample
  • Complex: Human CCAN complex with bound alpha-satellite DNA
    • Protein or peptide: Histone H3-like centromeric protein A
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-C
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (171-MER)
    • DNA: DNA (171-MER)
    • Protein or peptide: Centromere protein C
Function / homology
Function and homology information


spindle attachment to meiosis I kinetochore / inner kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis ...spindle attachment to meiosis I kinetochore / inner kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / chromosome segregation / RHO GTPases Activate Formins / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / kinetochore / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / structural constituent of chromatin / Transcriptional regulation of granulopoiesis / Separation of Sister Chromatids / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / midbody / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / cell division / negative regulation of cell population proliferation / chromatin binding / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein 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 / Histone H2B signature. / Histone H2B ...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 / 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 / RmlC-like jelly roll fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / 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 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein C / Histone H2A type 1-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsYatskevich S / Muir KW / Bellini D / Zhang Z / Yang J / Tischer T / Predin M / Dendooven T / McLaughlin SH / Barford D
Funding support United Kingdom, Germany, 3 items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
Boehringer Ingelheim Fonds (BIF) Germany
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Science / Year: 2022
Title: Structure of the human inner kinetochore bound to a centromeric CENP-A nucleosome.
Authors: Stanislau Yatskevich / Kyle W Muir / Dom Bellini / Ziguo Zhang / Jing Yang / Thomas Tischer / Masa Predin / Tom Dendooven / Stephen H McLaughlin / David Barford /
Abstract: Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron ...Kinetochores assemble onto specialized centromeric CENP-A (centromere protein A) nucleosomes (CENP-A) to mediate attachments between chromosomes and the mitotic spindle. We describe cryo-electron microscopy structures of the human inner kinetochore constitutive centromere associated network (CCAN) complex bound to CENP-A reconstituted onto α-satellite DNA. CCAN forms edge-on contacts with CENP-A, and a linker DNA segment of the α-satellite repeat emerges from the fully wrapped end of the nucleosome to thread through the central CENP-LN channel that tightly grips the DNA. The CENP-TWSX histone-fold module further augments DNA binding and partially wraps the linker DNA in a manner reminiscent of canonical nucleosomes. Our study suggests that the topological entrapment of the linker DNA by CCAN provides a robust mechanism by which kinetochores withstand both pushing and pulling forces exerted by the mitotic spindle.
History
DepositionFeb 11, 2022-
Header (metadata) releaseApr 27, 2022-
Map releaseApr 27, 2022-
UpdateJun 1, 2022-
Current statusJun 1, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14334.png

Downloads & links

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Map

FileDownload / File: emd_14334.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 360 pix.
= 307.08 Å		0.85 Å/pix.
x 360 pix.
= 307.08 Å		0.85 Å/pix.
x 360 pix.
= 307.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.853 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2446439 - 2.8596215
Average (Standard dev.)-0.0008152532 (±0.049154703)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 307.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human CCAN complex with bound alpha-satellite DNA

EntireName: Human CCAN complex with bound alpha-satellite DNA
Components
  • Complex: Human CCAN complex with bound alpha-satellite DNA
    • Protein or peptide: Histone H3-like centromeric protein A
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-C
    • Protein or peptide: Histone H2B type 1-C/E/F/G/I
    • DNA: DNA (171-MER)
    • DNA: DNA (171-MER)
    • Protein or peptide: Centromere protein C

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Supramolecule #1: Human CCAN complex with bound alpha-satellite DNA

SupramoleculeName: Human CCAN complex with bound alpha-satellite DNA / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Macromolecule #1: Histone H3-like centromeric protein A

MacromoleculeName: Histone H3-like centromeric protein A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.02363 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGPRRRSRKP EAPRRRSPSP TPTPGPSRRG PSLGASSHQH SRRRQGWLKE IRKLQKSTHL LIRKLPFSRL AREICVKFTR GVDFNWQAQ ALLALQEAAE AFLVHLFEDA YLLTLHAGRV TLFPKDVQLA RRIRGLEEGL G

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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: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

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Macromolecule #3: Histone H2A type 1-C

MacromoleculeName: Histone H2A type 1-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.135523 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAIR NDEELNKLLG RVTIAQGGVL PNIQAVLLPK KTESHHKAKG K

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.937213 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK

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Macromolecule #7: Centromere protein C

MacromoleculeName: Centromere protein C / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 61.724816 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: AASGLDHLKN GYRRRFCRPS RARDINTEQG QNVLEILQDC FEEKSLANDF STNSTKSVPN STRKIKDTCI QSPSKECQKS HPKSVPVSS KKKEASLQFV VEPSEATNRS VQAHEVHQKI LATDVSSKNT PDSKKISSRN INDHHSEADE EFYLSVGSPS V LLDAKTSV ...String:
AASGLDHLKN GYRRRFCRPS RARDINTEQG QNVLEILQDC FEEKSLANDF STNSTKSVPN STRKIKDTCI QSPSKECQKS HPKSVPVSS KKKEASLQFV VEPSEATNRS VQAHEVHQKI LATDVSSKNT PDSKKISSRN INDHHSEADE EFYLSVGSPS V LLDAKTSV SQNVIPSSAQ KRETYTFENS VNMLPSSTEV SVKTKKRLNF DDKVMLKKIE IDNKVSDEED KTSEGQERKP SG SSQNRIR DSEYEIQRQA KKSFSTLFLE TVKRKSESSP IVRHAATAPP HSCPPDDTKL IEDEFIIDES DQSFASRSWI TIP RKAGSL KQRTISPAES TALLQGRKSR EKHHNILPKT LANDKHSHKP HPVETSQPSD KTVLDTSYAL IGETVNNYRS TKYE MYSKN AEKPSRSKRT IKQKQRRKFM AKPAEEQLDV GQSKDENIHT SHITQDEFQR NSDRNMEEHE EMGNDCVSKK QMPPV GSKK SSTRKDKEES KKKRFSSESK NKLVPEEVTS TVTKSRRISR RPSDWWVVKS EESPVYSNS

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Macromolecule #5: DNA (171-MER)

MacromoleculeName: DNA (171-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.725812 KDa
SequenceString: (DT)(DC)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DC) (DC)(DA)(DA)(DT)(DT)(DC)(DC)(DA)(DG)(DA) (DT)(DA)(DC)(DT)(DA)(DC)(DA)(DA)(DA) (DA)(DA)(DG)(DA)(DG)(DT)(DG)(DT)(DT)(DT) (DC) (DA)(DA)(DA)(DA)(DC)(DT) ...String:
(DT)(DC)(DC)(DA)(DA)(DA)(DT)(DG)(DT)(DC) (DC)(DA)(DA)(DT)(DT)(DC)(DC)(DA)(DG)(DA) (DT)(DA)(DC)(DT)(DA)(DC)(DA)(DA)(DA) (DA)(DA)(DG)(DA)(DG)(DT)(DG)(DT)(DT)(DT) (DC) (DA)(DA)(DA)(DA)(DC)(DT)(DG)(DC) (DT)(DC)(DT)(DA)(DT)(DG)(DA)(DA)(DA)(DA) (DG)(DG) (DA)(DA)(DT)(DG)(DT)(DT)(DC) (DA)(DA)(DC)(DT)(DC)(DT)(DA)(DT)(DG)(DA) (DG)(DT)(DT) (DG)(DA)(DA)(DT)(DG)(DC) (DA)(DA)(DA)(DC)(DA)(DT)(DC)(DA)(DC)(DA) (DT)(DA)(DG)(DA) (DA)(DG)(DT)(DT)(DT) (DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT)(DG)(DC) (DT)(DT)(DC)(DT)(DG) (DT)(DC)(DT)(DA) (DG)(DT)(DT)(DT)(DT)(DT)(DA)(DT)(DG)(DT) (DG)(DA)(DA)(DC)(DA)(DT) (DA)(DT)(DT) (DC)(DC)(DC)(DG)(DT)(DT)(DT)(DC)(DC)(DA) (DA)(DC)(DG)(DA)(DA)(DG)(DG) (DC)(DC) (DT)(DC)(DA)(DA)(DA)(DG)(DC)(DG)(DG)

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Macromolecule #6: DNA (171-MER)

MacromoleculeName: DNA (171-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.822809 KDa
SequenceString: (DC)(DC)(DG)(DC)(DT)(DT)(DT)(DG)(DA)(DG) (DG)(DC)(DC)(DT)(DT)(DC)(DG)(DT)(DT)(DG) (DG)(DA)(DA)(DA)(DC)(DG)(DG)(DG)(DA) (DA)(DT)(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DC) (DA) (DT)(DA)(DA)(DA)(DA)(DA) ...String:
(DC)(DC)(DG)(DC)(DT)(DT)(DT)(DG)(DA)(DG) (DG)(DC)(DC)(DT)(DT)(DC)(DG)(DT)(DT)(DG) (DG)(DA)(DA)(DA)(DC)(DG)(DG)(DG)(DA) (DA)(DT)(DA)(DT)(DG)(DT)(DT)(DC)(DA)(DC) (DA) (DT)(DA)(DA)(DA)(DA)(DA)(DC)(DT) (DA)(DG)(DA)(DC)(DA)(DG)(DA)(DA)(DG)(DC) (DA)(DT) (DT)(DC)(DT)(DC)(DA)(DG)(DA) (DA)(DA)(DC)(DT)(DT)(DC)(DT)(DA)(DT)(DG) (DT)(DG)(DA) (DT)(DG)(DT)(DT)(DT)(DG) (DC)(DA)(DT)(DT)(DC)(DA)(DA)(DC)(DT)(DC) (DA)(DT)(DA)(DG) (DA)(DG)(DT)(DT)(DG) (DA)(DA)(DC)(DA)(DT)(DT)(DC)(DC)(DT)(DT) (DT)(DT)(DC)(DA)(DT) (DA)(DG)(DA)(DG) (DC)(DA)(DG)(DT)(DT)(DT)(DT)(DG)(DA)(DA) (DA)(DC)(DA)(DC)(DT)(DC) (DT)(DT)(DT) (DT)(DT)(DG)(DT)(DA)(DG)(DT)(DA)(DT)(DC) (DT)(DG)(DG)(DA)(DA)(DT)(DT) (DG)(DG) (DA)(DC)(DA)(DT)(DT)(DT)(DG)(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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 189204
FSC plot (resolution estimation)

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