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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
KeywordsChromosome / kinetochore / cell division / centromere / CELL CYCLE
Function / homology
Function and homology information


spindle attachment to meiosis I kinetochore / CENP-A containing chromatin assembly / centromeric DNA binding / kinetochore assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / inner kinetochore / establishment of mitotic spindle orientation / mitotic cytokinesis ...spindle attachment to meiosis I kinetochore / CENP-A containing chromatin assembly / centromeric DNA binding / kinetochore assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / inner kinetochore / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / pericentric heterochromatin / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / 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 / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Resolution of Sister Chromatid Cohesion / 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 / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / chromosome segregation / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / RHO GTPases Activate Formins / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / kinetochore / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / Separation of Sister Chromatids / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / mitotic cell cycle / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / midbody / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / defense response to Gram-positive bacterium / Ub-specific processing proteases / nuclear body / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / cell division / chromatin binding / protein-containing complex / extracellular space / DNA binding / RNA 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 H2B signature. / Histone H2A conserved site / Histone H2A 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 1-C
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.44 Å
AuthorsYatskevich S / Muir KW
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-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing 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 / 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

UniProtKB: Histone H3-like centromeric protein A

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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

UniProtKB: Histone H4

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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

UniProtKB: Histone H2A type 1-C

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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

UniProtKB: Histone H2B type 1-C/E/F/G/I

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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

UniProtKB: Centromere protein C

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

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Image processing

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

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