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- EMDB-55759: Structure of the human inner kinetochore CCAN bound to a di-CENP-... -

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Basic information

Entry
Database: EMDB / ID: EMD-55759
TitleStructure of the human inner kinetochore CCAN bound to a di-CENP-A nucleosome
Map data
Sample
  • Complex: Human inner kinetochore CCAN bound to a di-CENP-A nucleosome
    • Protein or peptide: x 19 types
  • Protein or peptide: x 1 types
  • DNA: x 2 types
KeywordsCentromeres / Kinetochores / CELL CYCLE
Function / homology
Function and homology information


MGMT-mediated DNA damage reversal / FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / kinetochore organization / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding ...MGMT-mediated DNA damage reversal / FANCM-MHF complex / Mis6-Sim4 complex / positive regulation of protein localization to kinetochore / kinetochore organization / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Fanconi anaemia nuclear complex / metaphase chromosome alignment / kinetochore binding / sex differentiation / chordate embryonic development / DNA-methyltransferase activity / resolution of meiotic recombination intermediates / CENP-A containing chromatin assembly / negative regulation of epithelial cell apoptotic process / protein localization to chromosome, centromeric region / kinetochore assembly / condensed chromosome, centromeric region / inner kinetochore / DNA alkylation repair / positive regulation of double-strand break repair / establishment of mitotic spindle orientation / mitotic cytokinesis / mitotic sister chromatid segregation / replication fork processing / chromosome, centromeric region / chromosome organization / pericentric heterochromatin / interstrand cross-link repair / 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 / Deposition of new CENPA-containing nucleosomes at the centromere / Mitotic Prometaphase / telomere organization / EML4 and NUDC in mitotic spindle formation / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / Assembly of the ORC complex at the origin of replication / NRIF signals cell death from the nucleus / Meiotic synapsis / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / Resolution of Sister Chromatid Cohesion / positive regulation of epithelial cell proliferation / positive regulation of protein ubiquitination / DNA methylation / Condensation of Prophase Chromosomes / mitotic spindle organization / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / methyltransferase activity / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / innate immune response in mucosa / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Fanconi Anemia Pathway / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / chromosome segregation / Transcriptional regulation by small RNAs / RHO GTPases Activate Formins / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / HDMs demethylate histones / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKR-mediated signaling / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / kinetochore / DNA Damage/Telomere Stress Induced Senescence / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / centriolar satellite / Metalloprotease DUBs / RMTs methylate histone arginines / nuclear matrix / HCMV Early Events / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide
Similarity search - Function
Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q ...Centromere protein W / : / CENP-W protein / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Centromere subunit L / Centromere protein L / Centromere protein R / Centromere protein Q / Centromere protein P / Kinetochore component, CENP-R / CENP-Q, a CENPA-CAD centromere complex subunit / CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P / Centromere protein H, C-terminal / Centromere protein Cenp-M / Centromere protein Cenp-K / Centromere protein H / Centromere protein H (CENP-H) / Centromere protein M (CENP-M) / Centromere-associated protein K / Centromere protein I / Mis6 / Centromere protein U / CENP-A nucleosome associated complex (NAC) subunit / Centromere protein X / CENP-S/Mhf1 / CENP-S associating Centromere protein X / CENP-S protein / Centromere protein O / : / Cenp-O kinetochore centromere component / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding domain / : / 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 / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Centromere protein X / Methylated-DNA--protein-cysteine methyltransferase / Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U / Centromere protein Q ...Centromere protein X / Methylated-DNA--protein-cysteine methyltransferase / Histone H3-like centromeric protein A / Histone H4 / Histone H2B type 1-C/E/F/G/I / Centromere protein R / Centromere protein W / Centromere protein P / Centromere protein U / Centromere protein Q / Centromere protein L / Centromere protein S / Centromere protein I / Histone H2A type 1-C / Centromere protein T / Centromere protein N / Centromere protein K / Centromere protein O / Centromere protein H / Centromere protein M
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.5 Å
AuthorsYu C / Barford D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120 United Kingdom
Cancer Research UKC576/A25675 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Models for the architecture of the human inner kinetochore on centromeric α-satellite CENP-A nucleosome arrays.
Authors: Cong Yu / Kyle W Muir / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / David Barford /
Abstract: Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp α-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled ...Human kinetochores assemble onto centromeric DNA comprising repetitive arrays of the 171 bp α-satellite sequence. To understand the higher-order architecture of the inner kinetochore assembled onto α-satellite arrays, we show cryo-EM structures of CCAN with free DNA, and α-satellite repeat monomers and dimers with CENP-A nucleosomes. CCAN bound to free DNA and a monomeric CENP-A nucleosome engages 70 bp of DNA comprising 30 bp of an upstream α-satellite repeat. This upstream DNA interacts with the histone-fold domain subunits of the CENP-TWSX module in a manner resembling how nucleosomes wrap DNA gyres. A complex of CCAN assembled onto a dimeric α-satellite repeat with two CENP-A nucleosomes shows that CCAN can only be accommodated on the linker DNA by unwrapping DNA from both the CENP-TWSX module and the upstream nucleosome. We discuss the implications of these results for models of CCAN assembly on arrays of α-satellite chromatin containing CENP-A nucleosomes.
History
DepositionNov 18, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55759.png

Downloads & links

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Map

FileDownload / File: emd_55759.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 400 pix.
= 371.2 Å		0.93 Å/pix.
x 400 pix.
= 371.2 Å		0.93 Å/pix.
x 400 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.928 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0015
Minimum - Maximum-0.0013963185 - 0.0059859743
Average (Standard dev.)0.000103226914 (±0.00045781521)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 371.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human inner kinetochore CCAN bound to a di-CENP-A nucleosome

EntireName: Human inner kinetochore CCAN bound to a di-CENP-A nucleosome
Components
  • Complex: Human inner kinetochore CCAN bound to a di-CENP-A nucleosome
    • Protein or peptide: Centromere protein H
    • Protein or peptide: Centromere protein I
    • Protein or peptide: Centromere protein K
    • Protein or peptide: Centromere protein L
    • Protein or peptide: Centromere protein M
    • Protein or peptide: Centromere protein N
    • Protein or peptide: Centromere protein O
    • Protein or peptide: Centromere protein Q
    • Protein or peptide: Centromere protein U
    • Protein or peptide: Centromere protein P
    • Protein or peptide: Centromere protein R
    • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T
    • Protein or peptide: Centromere protein W
    • Protein or peptide: Centromere protein S
    • Protein or peptide: Centromere protein X
    • 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: scFv
  • Protein or peptide: Histone H2B type 1-C/E/F/G/I
  • DNA: DNA (318-MER)
  • DNA: DNA (318-MER)

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Supramolecule #1: Human inner kinetochore CCAN bound to a di-CENP-A nucleosome

SupramoleculeName: Human inner kinetochore CCAN bound to a di-CENP-A nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18, #22
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Centromere protein H

MacromoleculeName: Centromere protein H / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.520941 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEEQPQMQDA DEPADSGGEG RAGGPPQVAG AQAACSEDRM TLLLRLRAQT KQQLLEYKSM VDASEEKTPE QIMQEKQIEA KIEDLENEI EEVKVAFEIK KLALDRMRLS TALKKNLEKI SRQSSVLMDN MKHLLELNKL IMKSQQESWD LEEKLLDIRK K RLQLKQAS ...String:
MEEQPQMQDA DEPADSGGEG RAGGPPQVAG AQAACSEDRM TLLLRLRAQT KQQLLEYKSM VDASEEKTPE QIMQEKQIEA KIEDLENEI EEVKVAFEIK KLALDRMRLS TALKKNLEKI SRQSSVLMDN MKHLLELNKL IMKSQQESWD LEEKLLDIRK K RLQLKQAS ESKLLEIQTE KNKQKIDLDS MENSERIKII RQNLQMEIKI TTVIQHVFQN LILGSKVNWA EDPALKEIVL QL EKNVDMM

UniProtKB: Centromere protein H

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Macromolecule #2: Centromere protein I

MacromoleculeName: Centromere protein I / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.615031 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSPQKRVKNV QAQNRTSQGS SSFQTTLSAW KVKQDPSNSK NISKHGQNNP VGDYEHADDQ AEEDALQMAV GYFEKGPIKA SQNKDKTLE KHLKTVENVA WKNGLASEEI DILLNIALSG KFGNAVNTRI LKCMIPATVI SEDSVVKAVS WLCVGKCSGS T KVLFYRWL ...String:
MSPQKRVKNV QAQNRTSQGS SSFQTTLSAW KVKQDPSNSK NISKHGQNNP VGDYEHADDQ AEEDALQMAV GYFEKGPIKA SQNKDKTLE KHLKTVENVA WKNGLASEEI DILLNIALSG KFGNAVNTRI LKCMIPATVI SEDSVVKAVS WLCVGKCSGS T KVLFYRWL VAMFDFIDRK EQINLLYGFF FASLQDDALC PYVCHLLYLL TKKENVKPFR VRKLLDLQAK MGMQPHLQAL LS LYKFFAP ALISVSLPVR KKIYFKNSEN LWKTALLAVK QRNRGPSPEP LKLMLGPANV RPLKRKWNSL SVIPVLNSSS YTK ECGKKE MSLSDCLNRS GSFPLEQLQS FPQLLQNIHC LELPSQMGSV LNNSLLLHYI NCVRDEPVLL RFYYWLSQTL QEEC IWYKV NNYEHGKEFT NFLDTIIRAE CFLQEGFYSC EAFLYKSLPL WDGLCCRSQF LQLVSWIPFS SFSEVKPLLF DHLAQ LFFT STIYFKCSVL QSLKELLQNW LLWLSMDIHM KPVTNSPLET TLGGSMNSVS KLIHYVGWLS TTAMRLESNN TFLLHF ILD FYEKVCDIYI NYNLPLVVLF PPGIFYSALL SLDTSILNQL CFIMHRYRKN LTAAKKNELV QKTKSEFNFS SKTYQEF NH YLTSMVGCLW TSKPFGKGIY IDPEILEKTG VAEYKNSLNV VHHPSFLSYA VSFLLQESPE ERTVNVSSIR GKKWSWYL D YLFSQGLQGL KLFIRSSVHH SSIPRAEGIN CNNQYENLYF Q

UniProtKB: Centromere protein I

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Macromolecule #3: Centromere protein K

MacromoleculeName: Centromere protein K / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.69607 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNQEDLDPDS TTDVGDVTNT EEELIRECEE MWKDMEECQN KLSLIGTETL TDSNAQLSLL IMQVKCLTAE LSQWQKKTPE TIPLTEDVL ITLGKEEFQK LRQDLEMVLS TKESKNEKLK EDLEREQRWL DEQQQIMESL NVLHSELKNK VETFSESRIF N ELKTKMLN ...String:
MNQEDLDPDS TTDVGDVTNT EEELIRECEE MWKDMEECQN KLSLIGTETL TDSNAQLSLL IMQVKCLTAE LSQWQKKTPE TIPLTEDVL ITLGKEEFQK LRQDLEMVLS TKESKNEKLK EDLEREQRWL DEQQQIMESL NVLHSELKNK VETFSESRIF N ELKTKMLN IKEYKEKLLS TLGEFLEDHF PLPDRSVKKK KKNIQESSVN LITLHEMLEI LINRLFDVPH DPYVKISDSF WP PYVELLL RNGIALRHPE DPTRIRLEAF HQ

UniProtKB: Centromere protein K

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Macromolecule #4: Centromere protein L

MacromoleculeName: Centromere protein L / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.364016 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPLGMDSYSA PESTPSASSR PEDYFIGATP LQKRLESVRK QSSFILTPPR RKIPQCSQLQ EDVDPQKVAF LLHKQWTLYS LTPLYKFSY SNLKEYSRLL NAFIVAEKQK GLAVEVGEDF NIKVIFSTLL GMKGTQRDPE AFLVQIVSKS QLPSENREGK V LWTGWFCC ...String:
GPLGMDSYSA PESTPSASSR PEDYFIGATP LQKRLESVRK QSSFILTPPR RKIPQCSQLQ EDVDPQKVAF LLHKQWTLYS LTPLYKFSY SNLKEYSRLL NAFIVAEKQK GLAVEVGEDF NIKVIFSTLL GMKGTQRDPE AFLVQIVSKS QLPSENREGK V LWTGWFCC VFGDSLLETV SEDFTCLPLF LANGAESNTA IIGTWFQKTF DCYFSPLAIN AFNLSWMAAM WTACKMDHYV AT TEFLWSV PCSPQSLDIS FAIHPEDAKA LWDSVHKTPG EVTQEEVDLF MDCLYSHFHR HFKIHLSATR LVRVSTSVAS AHT DGKIKI LCHKYLIGVL AYLTELAIFQ IE

UniProtKB: Centromere protein L

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Macromolecule #5: Centromere protein M

MacromoleculeName: Centromere protein M / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.761945 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MSVLRPLDKL PGLNTATILL VGTEDALLQQ LADSMLKEDC ASELKVHLAK SLPLPSSVNR PRIDLIVFVV NLHSKYSLQN TEESLRHVD ASFFLGKVCF LATGAGRESH CSIHRHTVVK LAHTYQSPLL YCDLEVEGFR ATMAQRLVRV LQICAGHVPG V SALNLLSL LRSSEGPSLE DL

UniProtKB: Centromere protein M

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Macromolecule #6: Centromere protein N

MacromoleculeName: Centromere protein N / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.541641 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWEVFQMS KGPGEDVDLF DMKQFKNSFK KILQRALKNV TVSFRETEEN AVWIRIAWGT QYTKPNQYKP TYVVYYSQTP Y AFTSSSML ...String:
MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWEVFQMS KGPGEDVDLF DMKQFKNSFK KILQRALKNV TVSFRETEEN AVWIRIAWGT QYTKPNQYKP TYVVYYSQTP Y AFTSSSML RRNTPLLGQA LTIASKHHQI VKMDLRSRYL DSLKAIVFKQ YNQTFETHNS TTPLQERSLG LDINMDSRII HE NIVEKER VQRITQETFG DYPQPQLEFA QYKLETKFKS GLNGSILAER KEPLRCLIKF SSPHLLEALK SLAPAGIADA PLS PLLTCI PNKRMNYFKI RDKSDLEVLF Q

UniProtKB: Centromere protein N

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Macromolecule #7: Centromere protein O

MacromoleculeName: Centromere protein O / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.830637 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MEQANPLRPD GESKGGVLAH LERLETQVSR SRKQSEELQS VQAQEGALGT KIHKLRRLRD ELRAVVRHRR ASVKACIANV EPNQTVEIN EQEALEEKLE NVKAILQAYH FTGLSGKLTS RGVCVCISTA FEGNLLDSYF VDLVIQKPLR IHHHSVPVFI P LEEIAAKY ...String:
MEQANPLRPD GESKGGVLAH LERLETQVSR SRKQSEELQS VQAQEGALGT KIHKLRRLRD ELRAVVRHRR ASVKACIANV EPNQTVEIN EQEALEEKLE NVKAILQAYH FTGLSGKLTS RGVCVCISTA FEGNLLDSYF VDLVIQKPLR IHHHSVPVFI P LEEIAAKY LQTNIQHFLF SLCEYLNAYS GRKYQADRLQ SDFAALLTGP LQRNPLCNLL SFTYKLDPGG QSFPFCARLL YK DLTATLP TDVTVTCQGV EVLSTSWEEQ RASHETLFCT KPLHQVFASF TRKGEKLDMS LVS

UniProtKB: Centromere protein O

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Macromolecule #8: Centromere protein Q

MacromoleculeName: Centromere protein Q / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.634549 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MTKHTNLKHG KTAASKRKTW QPLSKSTRDH LQTMMESVIM TILSNSIKEK EEIQYHLNFL KKRLLQQCET LKVPPKKMED LTNVSSLLN MERARDKANE EGLALLQEEI DKMVETTELM TGNIQSLKNK IQILASEVEE EEERVKQMHQ INSSGVLSLP E LSQKTLKA ...String:
MTKHTNLKHG KTAASKRKTW QPLSKSTRDH LQTMMESVIM TILSNSIKEK EEIQYHLNFL KKRLLQQCET LKVPPKKMED LTNVSSLLN MERARDKANE EGLALLQEEI DKMVETTELM TGNIQSLKNK IQILASEVEE EEERVKQMHQ INSSGVLSLP E LSQKTLKA PTLQKEILAL IPNQNALLKD LDILHNSSQM KSMSTFIEEA YKKLDAS

UniProtKB: Centromere protein Q

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Macromolecule #9: Centromere protein U

MacromoleculeName: Centromere protein U / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.484873 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKTSDIKELN IVLPEFEKTH LEHQQRIESK VCKAAIATFY VNVKEQFIKM LKESQMLTNL KRKNAKMISD IEKKRQRMIE VQDELLRLE PQLKQLQTKY DELKERKSSL RNAAYFLSNL KQLYQDYSDV QAQEPNVKET YDSSSLPALL FKARTLLGAE S HLRNINHQ ...String:
MKTSDIKELN IVLPEFEKTH LEHQQRIESK VCKAAIATFY VNVKEQFIKM LKESQMLTNL KRKNAKMISD IEKKRQRMIE VQDELLRLE PQLKQLQTKY DELKERKSSL RNAAYFLSNL KQLYQDYSDV QAQEPNVKET YDSSSLPALL FKARTLLGAE S HLRNINHQ LEKLLDQGEN LYFQSWSHPQ FEKGGGSGGG SGGGSWSHPQ FEK

UniProtKB: Centromere protein U

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Macromolecule #10: Centromere protein P

MacromoleculeName: Centromere protein P / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.210949 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDAELAEVRA LQAEIAALRR ACEDPPAPWE EKSRVQKSFQ AIHQFNLEGW KSSKDLKNQL GHLESELSFL STLTGINIRN HSKQTEDLT STEMTEKSIR KVLQRHRLSG NCHMVTFQLE FQILEIQNKE RLSSAVTDLN IIMEPTECSE LSEFVSRAEE R KDLFMFFR ...String:
MDAELAEVRA LQAEIAALRR ACEDPPAPWE EKSRVQKSFQ AIHQFNLEGW KSSKDLKNQL GHLESELSFL STLTGINIRN HSKQTEDLT STEMTEKSIR KVLQRHRLSG NCHMVTFQLE FQILEIQNKE RLSSAVTDLN IIMEPTECSE LSEFVSRAEE R KDLFMFFR SLHFFVEWFE YRKRTFKHLK EKYPDAVYLS EGPSSCSMGI RSASRPGFEL VIVWRIQIDE DGKVFPKLDL LT KVPQRAL ELDKNRAIET APLSFRTLVG LLGIEAALES LIKSLCAEEN N

UniProtKB: Centromere protein P

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Macromolecule #11: Centromere protein R

MacromoleculeName: Centromere protein R / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.228297 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MPVKRSLKLD GLLEENSFDP SKITRKKSVI TYSPTTGTCQ MSLFASPTSS EEQKHRNGLS NEKRKKLNHP SLTESKESTT KDNDEFMML LSKVEKLSEE IMEIMQNLSS IQALEGSREL ENLIGISCAS HFLKREMQKT KELMTKVNKQ KLFEKSTGLP H KASRHLDS YEFLKAILN

UniProtKB: Centromere protein R

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Macromolecule #12: Methylated-DNA--protein-cysteine methyltransferase,Centromere pro...

MacromoleculeName: Methylated-DNA--protein-cysteine methyltransferase,Centromere protein T
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 84.06768 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSYYHHHHHH DYDIPTTENL YFQGMDKDCE MKRTTLDSPL GKLELSGCEQ GLHRIIFLGK GTSAADAVEV PAPAAVLGGP EPLMQATAW LNAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYS HLAALAGNPA ATAAVKTALS G NPVPILIP ...String:
MSYYHHHHHH DYDIPTTENL YFQGMDKDCE MKRTTLDSPL GKLELSGCEQ GLHRIIFLGK GTSAADAVEV PAPAAVLGGP EPLMQATAW LNAYFHQPEA IEEFPVPALH HPVFQQESFT RQVLWKLLKV VKFGEVISYS HLAALAGNPA ATAAVKTALS G NPVPILIP CHRVVQGDLD VGGYEGGLAV KEWLLAHEGH RLGKPGLGSD LEVLFQGPMA DHNPDSDSTP RTLLRRVLDT AD PRTPRRP RSARAGARRA LLETASPRKL SGQTRTIARG RSHGARSVGR SAHIQASGHL EEQTPRTLLK NILLTAPESS ILM PESVVK PVPAPQAVQP SRQESSCGSL ELQLPELEPP TTLAPGLLAP GRRKQRLRLS VFQQGVDQGL SLSQEPQGNA DASS LTRSL NLTFATPLQP QSVQRPGLAR RPPARRAVDV GAFLRDLRDT SLAPPNIVLE DTQPFSQPMV GSPNVYHSLP CTPHT GAED AEQAAGRKTQ SSGPGLQKNS PGKPAQFLAG EAEEVNAFAL GFLSTSSGVS GEDEVEPLHD GVEEAEKKME EEGVSV SEM EATGAQGPSR VEEAEGHTEV TEAEGSQGTA EADGPGASSG DEDASGRAAS PESASSTPES LQARRHHQFL EPAPAPG AA VLSSEPAEPL LVRHPPRPRT TGPRPRQDPH KAGLSHYVKL FSFYAKMPME RKALEMVEKC LDKYFQHLCD DLEVFAAH A GRKTVKPEDL ELLMRRQGLV TDQVSLHVLV ERHLPLEYRQ LLIPCAYSGN SVFPAQ

UniProtKB: Methylated-DNA--protein-cysteine methyltransferase, Centromere protein T

+
Macromolecule #13: Centromere protein W

MacromoleculeName: Centromere protein W / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.087236 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MALSTIVSQR KQIKRKAPRG FLKRVFKRKK PQLRLEKSGD LLVHLNCLLF VHRLAEESRT NACASKCRVI NKEHVLAAAK VILKKSRG

UniProtKB: Centromere protein W

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Macromolecule #14: Centromere protein S

MacromoleculeName: Centromere protein S / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.917875 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MEEEAETEEQ QRFSYQQRLK AAVHYTVGCL CEEVALDKEM QFSKQTIAAI SELTFRQCEN FAKDLEMFAR HAKRTTINTE DVKLLARRS NSLLKYITDK SEEIAQINLE RKAQKKKKSE DGSKNSRQPA EAGVVESEN

UniProtKB: Centromere protein S

+
Macromolecule #15: Centromere protein X

MacromoleculeName: Centromere protein X / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.972415 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
MEGAGAGSGF RKELVSRLLH LHFKDDKTKV SGDALQLMVE LLKVFVVEAA VRGVRQAQAE DALRVDVDQL EKVLPQLLLD F

UniProtKB: Centromere protein X

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Macromolecule #16: Histone H3-like centromeric protein A

MacromoleculeName: Histone H3-like centromeric protein A / type: protein_or_peptide / ID: 16 / Number of copies: 4 / 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

+
Macromolecule #17: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 17 / Number of copies: 4 / 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

+
Macromolecule #18: Histone H2A type 1-C

MacromoleculeName: Histone H2A type 1-C / type: protein_or_peptide / ID: 18 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.666334 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SPGLEVLFQG PRGMSGRGKQ GGKARAKAKS RSSRAGLQFP VGRVHRLLRK GNYAERVGAG APVYLAAVLE YLTAEILEL AGNAARDNKK TRIIPRHLQL AIRNDEELNK LLGRVTIAQG GVLPNIQAVL LPKKTESHHK AKGK

UniProtKB: Histone H2A type 1-C

+
Macromolecule #19: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 19 / Number of copies: 4 / 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

+
Macromolecule #22: scFv

MacromoleculeName: scFv / type: protein_or_peptide / ID: 22 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 29.16134 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MMKSSHHHHH HENLYFQSNA MEVQLQQSGP ELVEPGTSVK MPCKASGYTF TSYTIQWVKQ TPRQGLEWIG YIYPYNAGTK YNEKFKGKA TLTSDKSSST VYMELSSLTS EDSAVYYCAR KSSRLRSTLD YWGQGTSVTV SSGGGGSGGG GSGGGGSMDI K MTQSPSSM ...String:
MMKSSHHHHH HENLYFQSNA MEVQLQQSGP ELVEPGTSVK MPCKASGYTF TSYTIQWVKQ TPRQGLEWIG YIYPYNAGTK YNEKFKGKA TLTSDKSSST VYMELSSLTS EDSAVYYCAR KSSRLRSTLD YWGQGTSVTV SSGGGGSGGG GSGGGGSMDI K MTQSPSSM HASLGERVTI TCKASQDIRS YLSWYQQKPW KSPKTLIYYA TSLADGVPSR FSGSGSGQDF SLTINNLESD DT ATYYCLQ HGESPYTFGS GTKLEIKRA

+
Macromolecule #20: DNA (318-MER)

MacromoleculeName: DNA (318-MER) / type: dna / ID: 20 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.810586 KDa
SequenceString: (DA)(DT)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DT) (DA)(DT)(DC)(DT)(DT)(DC)(DA)(DC)(DA)(DT) (DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DG) (DA)(DC)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC) (DG) (DT)(DA)(DG)(DA)(DC)(DA) ...String:
(DA)(DT)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DT) (DA)(DT)(DC)(DT)(DT)(DC)(DA)(DC)(DA)(DT) (DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DG) (DA)(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)(DT)(DT) (DG)(DT)(DA)(DG)(DT)(DA)(DT)(DC)(DT)(DG) (DC)(DA)(DA)(DG)(DT)(DG) (DG)(DA)(DC) (DA)(DT)(DT)(DC)(DG)(DG)(DA)(DG)(DC)(DA) (DC)(DT)(DT)(DT)(DG)(DT)(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)(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)(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)(DG)(DA)(DT)

+
Macromolecule #21: DNA (318-MER)

MacromoleculeName: DNA (318-MER) / type: dna / ID: 21 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 100.290844 KDa
SequenceString: (DA)(DT)(DC)(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)(DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA) (DG) (DG)(DG)(DA)(DG)(DT)(DA) ...String:
(DA)(DT)(DC)(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)(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)(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)(DA)(DC)(DA)(DA)(DA)(DG)(DT) (DG)(DC)(DT)(DC)(DC)(DG)(DA)(DA) (DT) (DG)(DT)(DC)(DC)(DA)(DC)(DT)(DT)(DG)(DC) (DA)(DG)(DA)(DT)(DA)(DC)(DT)(DA)(DC) (DA)(DA)(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)(DT)(DC) (DT)(DA)(DG)(DT) (DT)(DT)(DT)(DT)(DA) (DT)(DG)(DT)(DG)(DA)(DA)(DG)(DA)(DT)(DA) (DT)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DT)

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 15057
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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