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- EMDB-4579: Structure of inner kinetochore CCAN-Cenp-A complex -

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Basic information

Entry
Database: EMDB / ID: EMD-4579
TitleStructure of inner kinetochore CCAN-Cenp-A complex
Map dataMap of CCAN-Cenp-A
Sample
  • Complex: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
    • Complex: kinetochore
      • Protein or peptide: x 12 types
    • Complex: DNA
      • DNA: x 2 types
    • Complex: Histones
      • Protein or peptide: x 7 types
Keywordsinner kinetochore / DNA / nucleosome / DNA BINDING PROTEIN
Function / homology
Function and homology information


2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / PKMTs methylate histone lysines / HDMs demethylate histones / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation ...2-micrometer circle DNA / 2-micrometer plasmid partitioning / negative regulation of meiotic DNA double-strand break formation involved in reciprocal meiotic recombination / COMA complex / maintenance of meiotic sister chromatid cohesion / PKMTs methylate histone lysines / HDMs demethylate histones / Mis6-Sim4 complex / centromere complex assembly / meiotic sister chromatid segregation / spindle attachment to meiosis I kinetochore / ascospore formation / establishment of meiotic sister chromatid cohesion / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / attachment of spindle microtubules to kinetochore / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / CENP-A containing chromatin assembly / centromeric DNA binding / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / outer kinetochore / kinetochore assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / establishment of mitotic sister chromatid cohesion / condensed chromosome, centromeric region / protein localization to kinetochore / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / replication fork protection complex / Oxidative Stress Induced Senescence / spindle pole body / RMTs methylate histone arginines / postreplication repair / SUMOylation of chromatin organization proteins / mitotic spindle assembly checkpoint signaling / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / mitotic sister chromatid segregation / DNA replication initiation / Ub-specific processing proteases / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / mitotic spindle organization / meiotic cell cycle / chromosome segregation / kinetochore / structural constituent of chromatin / nucleosome / peroxisome / heterochromatin formation / nucleosome assembly / mitotic cell cycle / chromatin organization / sequence-specific DNA binding / protein heterodimerization activity / cell division / DNA repair / regulation of DNA-templated transcription / protein-containing complex binding / structural molecule activity / negative regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Kinetochore subunit Nkp2/Cnl2 / Cnl2/NKP2 family protein / : / : / CENPH protein / CENPU protein / Centromere protein O / Cenp-O kinetochore centromere component ...Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Kinetochore subunit Nkp2/Cnl2 / Cnl2/NKP2 family protein / : / : / CENPH protein / CENPU protein / Centromere protein O / Cenp-O kinetochore centromere component / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / : / Histone H2B signature. / Histone H2B / Histone H2B / RmlC-like jelly roll fold / 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 / 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 H2B.1 / Histone H2B.2 / Histone H4 / Histone H2A.1 / Inner kinetochore subunit MIF2 / Histone H3-like centromeric protein CSE4 / Inner kinetochore subunit IML3 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit MCM22 ...Histone H2B.1 / Histone H2B.2 / Histone H4 / Histone H2A.1 / Inner kinetochore subunit MIF2 / Histone H3-like centromeric protein CSE4 / Inner kinetochore subunit IML3 / Inner kinetochore subunit AME1 / Inner kinetochore subunit CHL4 / Inner kinetochore subunit MCM22 / Inner kinetochore subunit OKP1 / Inner kinetochore subunit CTF19 / Inner kinetochore subunit NKP2 / Inner kinetochore subunit MCM21 / Inner kinetochore subunit MCM16 / Inner kinetochore subunit NKP1 / Inner kinetochore subunit CTF3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) cerevisiae (yeast) / Escherichia coli (E. coli) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsYan K / Yang J
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
European CommissionINFRAIA project Epic-XS (Project 823839)
CitationJournal: Nature / Year: 2019
Title: Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome.
Authors: Kaige Yan / Jing Yang / Ziguo Zhang / Stephen H McLaughlin / Leifu Chang / Domenico Fasci / Ann E Ehrenhofer-Murray / Albert J R Heck / David Barford /
Abstract: In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized ...In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes, function to connect centromeric chromatin to microtubules of the mitotic spindle. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-A), each of which is perfectly centred on its cognate centromere. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-A). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-A to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-A are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-A. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation.
History
DepositionJan 31, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseOct 2, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6qld
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4579.png

Downloads & links

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Map

FileDownload / File: emd_4579.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of CCAN-Cenp-A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 320 pix.
= 348.8 Å		1.09 Å/pix.
x 320 pix.
= 348.8 Å		1.09 Å/pix.
x 320 pix.
= 348.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.06863052 - 0.12158532
Average (Standard dev.)0.00029283442 (±0.0026867972)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 348.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z348.800348.800348.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0690.1220.000

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Supplemental data

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Sample components

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Entire : Inner kinetochore CCAN complex assembled onto a centromeric nucleosome

EntireName: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
Components
  • Complex: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
    • Complex: kinetochore
      • Protein or peptide: Inner kinetochore subunit MIF2
      • Protein or peptide: Inner kinetochore subunit MCM16
      • Protein or peptide: Inner kinetochore subunit CTF3
      • Protein or peptide: Inner kinetochore subunit MCM22
      • Protein or peptide: Inner kinetochore subunit IML3
      • Protein or peptide: Inner kinetochore subunit CHL4
      • Protein or peptide: Inner kinetochore subunit MCM21
      • Protein or peptide: Inner kinetochore subunit CTF19
      • Protein or peptide: Inner kinetochore subunit OKP1
      • Protein or peptide: Inner kinetochore subunit AME1
      • Protein or peptide: Inner kinetochore subunit NKP1
      • Protein or peptide: Inner kinetochore subunit NKP2
    • Complex: DNA
      • DNA: DNA (125-MER)
      • DNA: DNA (125-MER)
    • Complex: Histones
      • Protein or peptide: Histone H3-like centromeric protein CSE4
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2B.2
      • Protein or peptide: Histone H3-like centromeric protein CSE4
      • Protein or peptide: Histone H2A.1
      • Protein or peptide: Histone H2B.1
      • Protein or peptide: Histone H2A.1

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Supramolecule #1: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome

SupramoleculeName: Inner kinetochore CCAN complex assembled onto a centromeric nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17

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Supramolecule #2: kinetochore

SupramoleculeName: kinetochore / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3-#4, #6-#14
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) cerevisiae (yeast)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2, #5
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #4: Histones

SupramoleculeName: Histones / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #15-#21
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

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Macromolecule #1: Inner kinetochore subunit MIF2

MacromoleculeName: Inner kinetochore subunit MIF2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 2.754279 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
LRKSTRVKVA PLQYWRNEKI VY

UniProtKB: Inner kinetochore subunit MIF2

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Macromolecule #3: Inner kinetochore subunit MCM16

MacromoleculeName: Inner kinetochore subunit MCM16 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.815147 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
SSEKQWERIQ QLEKEHVEVY RELLITLDRL YLIRKHNHAV ILSHTQQRLL EIRHQLQINL EKTALLIRLL EKPDNTNVLF TKLQNLLEE SNSLDYELLQ SLGAQSSLHK QLIESRAERD ELMSKLIELS SKFP

UniProtKB: Inner kinetochore subunit MCM16

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Macromolecule #4: Inner kinetochore subunit CTF3

MacromoleculeName: Inner kinetochore subunit CTF3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 47.222789 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: NSNVLLPRKV MSRDSLKHLY SSIILIKNSR DESSSPYEWC IWQLKRCFAH QIETPQEVIP IIISVSSMDN KLSSRIIQTF CNLKYLKLD ELTLKKVCGG ILPLWKPELI SGTREFFVKF MASIFMWSTR DGHDNNCTFS ETCFYVLQMI TNWVLDDKLI A LGLTLLHD ...String:
NSNVLLPRKV MSRDSLKHLY SSIILIKNSR DESSSPYEWC IWQLKRCFAH QIETPQEVIP IIISVSSMDN KLSSRIIQTF CNLKYLKLD ELTLKKVCGG ILPLWKPELI SGTREFFVKF MASIFMWSTR DGHDNNCTFS ETCFYVLQMI TNWVLDDKLI A LGLTLLHD MQSLLTLDKI FNNATSNRFS TMAFISSLDI LTQLSKQTKS DYAIQYLIVG PDIMNKVFSS DDPLLLSAAC RY LVATKNK LMQYPSTNKF VRMQNQYIMD LTNYLYRNKV LSSKSLFGVS PDFFKQILEN LYIPTADFKN AKFFTITGIP ALS YICIII LRRLETAENT KIKFTSGIIN EETFNNFFRV HHDEIGQHGW IKGVNNIHDL RVKILMHLSN TANPYRDIAA FLFT YLKSL SKY

UniProtKB: Inner kinetochore subunit CTF3

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Macromolecule #6: Inner kinetochore subunit MCM22

MacromoleculeName: Inner kinetochore subunit MCM22 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.082116 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
VLDVYIKNLE NQIGNKRYFL KQAQGAIDEI TKRSLDTEGK PVNSEVFTEL LRKPMFFSER ADPIGFSLTS NFLSLRAQSS SEWLSLMND QSVDQKAMLL LQNNINSDLK ELLRKLQHQM TIM

UniProtKB: Inner kinetochore subunit MCM22

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Macromolecule #7: Inner kinetochore subunit IML3

MacromoleculeName: Inner kinetochore subunit IML3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.64473 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: PYTWKFLGIS KQLSLENGIA KLNQLLNLEV DLDIQTIRVP SDPDGGTAAD EYIRYEMRLD ISNLDEGTYS KFIFLGNSKM EVPMFLCYC GTDNRNEVVL QWLKAEYGVI MWPIKFEQKT MIKLADASIV HVTKENIEQI TWFSSKLYFE PETQDKNLRQ F SIEIPRES ...String:
PYTWKFLGIS KQLSLENGIA KLNQLLNLEV DLDIQTIRVP SDPDGGTAAD EYIRYEMRLD ISNLDEGTYS KFIFLGNSKM EVPMFLCYC GTDNRNEVVL QWLKAEYGVI MWPIKFEQKT MIKLADASIV HVTKENIEQI TWFSSKLYFE PETQDKNLRQ F SIEIPRES CEGLALGYGN TMHPYNDAIV PYIYNETGMA VERLPLTSVI LAGHTKIMRE SIVTSTRSLR NRVLAVVLQS IQ F

UniProtKB: Inner kinetochore subunit IML3

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Macromolecule #8: Inner kinetochore subunit CHL4

MacromoleculeName: Inner kinetochore subunit CHL4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 51.64243 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: LRLEDNYVPT SDTLVVFKQL MKLPVTVLYD LTLSWFAKFG GSFDGDIYLL TETLDLLIEK GVRRNVIVNR ILYVYWPDGL NVFQLAEID CHLMISKPEK FKWLPSKALR GDGKPYVVKL QPAKFIENLQ TDLAKIYHCH VYMFKHPSLP VLITRIQLFD S NNLFLSTP ...String:
LRLEDNYVPT SDTLVVFKQL MKLPVTVLYD LTLSWFAKFG GSFDGDIYLL TETLDLLIEK GVRRNVIVNR ILYVYWPDGL NVFQLAEID CHLMISKPEK FKWLPSKALR GDGKPYVVKL QPAKFIENLQ TDLAKIYHCH VYMFKHPSLP VLITRIQLFD S NNLFLSTP NIGSINKESL YNKLDKFQGK PLISRRPYYV AFPLNSPIIF HSVDKDIYAR LVLQSISRTI SERETIIFKP VQ KIPVKSI HNIMTLLGPS RFAESMGPWE CYASANFERS PLHDYKKHQG LTGKKVMVRE FDDSFLNDDE NFYGKEEPEI RRL RLEKNM IKFKGSANGV MDQKYNDLKE FNEHVHNIRN GKKNEDSGEP VYISRYSSLV PIEKVGFTLK NEINSRIITI KLKF NGNDI FGGLHELCDK NLINIDKVPG WLAGENGSFS GTIMNGDFQR EQ

UniProtKB: Inner kinetochore subunit CHL4

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Macromolecule #9: Inner kinetochore subunit MCM21

MacromoleculeName: Inner kinetochore subunit MCM21 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 24.746383 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: STSDRSELED YIVLENVYRM FGITFFPLVD PIDLKIKDAS GEIFVDREML GIRLEVFSER TSQFEKPHYV LLKKRIKSNS WFLFKHTIP SFIDVQGIFD DTNGGLVISH DDAYLFAKRV FLQLVEVQKR RQIFKDLEAK KIIHDLDLDL ESSMVSFFVK D IKVELFVK ...String:
STSDRSELED YIVLENVYRM FGITFFPLVD PIDLKIKDAS GEIFVDREML GIRLEVFSER TSQFEKPHYV LLKKRIKSNS WFLFKHTIP SFIDVQGIFD DTNGGLVISH DDAYLFAKRV FLQLVEVQKR RQIFKDLEAK KIIHDLDLDL ESSMVSFFVK D IKVELFVK QNEIVSCSIL DDIHDFSQNN KSKWEIALLG SLDDLELKLN HSFA

UniProtKB: Inner kinetochore subunit MCM21

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Macromolecule #10: Inner kinetochore subunit CTF19

MacromoleculeName: Inner kinetochore subunit CTF19 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 31.659006 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: QNDITQDFLN LISISSSNPN SAISDRKRVE RINGLTNLQK ELVTKYDTLP LLNMNLRLSY LRDHTYPHLQ VSVQSRDRVH NDGIEVLVV NYKFCRNTMN PFEIQFKMFY KFEDSTLLKW EILRISTNVR LKAKQLLATR NFQKCLLSLY EFDKIKSKKT G IFQNLINL ...String:
QNDITQDFLN LISISSSNPN SAISDRKRVE RINGLTNLQK ELVTKYDTLP LLNMNLRLSY LRDHTYPHLQ VSVQSRDRVH NDGIEVLVV NYKFCRNTMN PFEIQFKMFY KFEDSTLLKW EILRISTNVR LKAKQLLATR NFQKCLLSLY EFDKIKSKKT G IFQNLINL LKRKTRCYLM NNSDSLIVER VIREGRLTTI KLQINFIITM PGERGKPRNC FLPMSKISIA LWKGGERFNQ ID LDEICYG LIKEYGVKTG LKEICNVCLF PDM

UniProtKB: Inner kinetochore subunit CTF19

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Macromolecule #11: Inner kinetochore subunit OKP1

MacromoleculeName: Inner kinetochore subunit OKP1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 27.358393 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SILRLLETNT VSALDSVFEK YEKEMNQMTH GDNNEVKRIY SKKERLLEII LTKIKKKLRQ AKFPSRISER DLDIEYIYSK RQFIQNRYS QELQNNERLE AILSREQNLL EETRKLCMNL KTNNKKRLTE KLIQKDLHPV LNKAMEYTYG LESTNGFMHP D GPVTFRND ...String:
SILRLLETNT VSALDSVFEK YEKEMNQMTH GDNNEVKRIY SKKERLLEII LTKIKKKLRQ AKFPSRISER DLDIEYIYSK RQFIQNRYS QELQNNERLE AILSREQNLL EETRKLCMNL KTNNKKRLTE KLIQKDLHPV LNKAMEYTYG LESTNGFMHP D GPVTFRND SHELNLMLND PIKSTADVRL DKEEVLSLLP SLKEYTKKSK ELKETMGQMI SDSHEEEIKE VFV

UniProtKB: Inner kinetochore subunit OKP1

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Macromolecule #12: Inner kinetochore subunit AME1

MacromoleculeName: Inner kinetochore subunit AME1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 22.157994 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
SVTTIDVLSS LFINLFENDL IPQALKDFNK SDDDQFRKLL YKLDLRLFQT ISDQMTRDLK DILDINVSNN ELCYQLKQVL ARKEDLNQQ IISVRNEIQE LKAGKDWHDL QNEQAKLNDK VKLNKRLNDL TSTLLGKYEG DRKIMSQDSE DDSIRDDSNI L DIAHFVDL MDPYNGLLKK INKINENLSN EL

UniProtKB: Inner kinetochore subunit AME1

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Macromolecule #13: Inner kinetochore subunit NKP1

MacromoleculeName: Inner kinetochore subunit NKP1 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 26.875254 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: TDTYNSISNF IENELTALLS SDDYLMDDLA GELPNEVCRL LKAQVIEKRK DAMSRGKQDL LSKEIYDNES ELRASQSQQI MELVGDIPK YSLGSELRNR VEGEPQSTSI ERLIEDVLKL PQMEVADEEE VEVENDLKVL SEYSNLRKDL ILKCQALQIG E SKLSDILS ...String:
TDTYNSISNF IENELTALLS SDDYLMDDLA GELPNEVCRL LKAQVIEKRK DAMSRGKQDL LSKEIYDNES ELRASQSQQI MELVGDIPK YSLGSELRNR VEGEPQSTSI ERLIEDVLKL PQMEVADEEE VEVENDLKVL SEYSNLRKDL ILKCQALQIG E SKLSDILS QTNSINSLTT SIKEASEDDD ISEYFATYNG KLVVALEEMK LLLEEAVKTF GNSPEKREKI KKILSELKK

UniProtKB: Inner kinetochore subunit NKP1

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Macromolecule #14: Inner kinetochore subunit NKP2

MacromoleculeName: Inner kinetochore subunit NKP2 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 17.631734 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
SEQLLHNYVS DSLLTTLISF QEFKQQLQSY TSDEQQLQHW YELLQARDAR VTSELEARIK QFFITLRSRL LRFLESEQLS HSLSLETLI DALYKINDLL QQRLQILDDA IQEKTSELAE FENMVRSPSA GDNAIPGLLQ IIQSYINLLE EN

UniProtKB: Inner kinetochore subunit NKP2

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Macromolecule #15: Histone H3-like centromeric protein CSE4

MacromoleculeName: Histone H3-like centromeric protein CSE4 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.535404 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
LALYEIRKYQ RSTDLLISKI PFARLVKEVT DEFTTKDQDL RWQSMAIMAL QEASEAYLVG LLEHTNLLAL HAKRITIMKK DMQLARRIR G

UniProtKB: Histone H3-like centromeric protein CSE4

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Macromolecule #16: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 8.897329 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DNIQGITKPA IRRLARRGGV KRISGLIYEE VRAVLKSFLE SVIRDSVTYT EHAKRKTVTS LDVVYALKRQ GRTLYGFGG

UniProtKB: Histone H4

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Macromolecule #17: Histone H2B.2

MacromoleculeName: Histone H2B.2 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.342754 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RKETYSSYIY KVLKQTHPDT GISQKSMSIL NSFVNDIFER IATEASKLAA YNKKSTISAR EIQTAVRLIL PGELAKHAVS EGTRAVTKY SSST

UniProtKB: Histone H2B.2

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Macromolecule #18: Histone H3-like centromeric protein CSE4

MacromoleculeName: Histone H3-like centromeric protein CSE4 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 13.715144 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VRQKRREKQR KQSLKRVEKK YTPSELALYE IRKYQRSTDL LISKIPFARL VKEVTDEFTT KDQDLRWQSM AIMALQEASE AYLVGLLEH TNLLALHAKR ITIMKKDMQL ARRIRG

UniProtKB: Histone H3-like centromeric protein CSE4

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Macromolecule #19: Histone H2A.1

MacromoleculeName: Histone H2A.1 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 11.546386 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QSRSAKAGLT FPVGRVHRLL RRGNYAQRIG SGAPVYLTAV LEYLAAEILE LAGNAARDNK KTRIIPRHLQ LAIRNDDELN KLLGNVTIA QGGVLPNIHQ NLLPKK

UniProtKB: Histone H2A.1

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Macromolecule #20: Histone H2B.1

MacromoleculeName: Histone H2B.1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 10.413832 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARKETYSSYI YKVLKQTHPD TGISQKSMSI LNSFVNDIFE RIATEASKLA AYNKKSTISA REIQTAVRLI LPGELAKHAV SEGTRAVTK YSSST

UniProtKB: Histone H2B.1

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Macromolecule #21: Histone H2A.1

MacromoleculeName: Histone H2A.1 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 11.190911 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QSRSAKAGLT FPVGRVHRLL RRGNYAQRIG SGAPVYLTAV LEYLAAEILE LAGNAARDNK KTRIIPRHLQ LAIRNDDELN KLLGNVTIA QGGVLPNIHQ NLL

UniProtKB: Histone H2A.1

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Macromolecule #2: DNA (125-MER)

MacromoleculeName: DNA (125-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 38.030211 KDa
SequenceString: (DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA)(DG) (DA) (DC)(DA)(DG)(DC)(DT)(DC) ...String:
(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DC) (DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA)(DG) (DG)(DC)(DC)(DG)(DC)(DT)(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)(DA)(DG) (DG)(DC)(DA)(DC)

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Macromolecule #5: DNA (125-MER)

MacromoleculeName: DNA (125-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 38.510504 KDa
SequenceString: (DG)(DT)(DG)(DC)(DC)(DT)(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) ...String:
(DG)(DT)(DG)(DC)(DC)(DT)(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)(DA)(DG) (DC)(DG)(DG)(DC)(DC) (DT)(DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG) (DG)(DA)(DT)(DT)(DC) (DT)(DC)(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

Concentration1.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 32.0 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

Startup modelType of model: OTHER / Details: Reconstruction using SIMPLE_prime
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 145783
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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