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- EMDB-12993: Cenp-A nucleosome in complex with Cenp-C -

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Basic information

Entry
Database: EMDB / ID: EMD-12993
TitleCenp-A nucleosome in complex with Cenp-C
Map data
Sample
  • Complex: Cenp-A nucleosome in complex with Cenp-C
    • Complex: Kinetochore subunit
      • Protein or peptide: BJ4_G0006610.mRNA.1.CDS.1
    • Complex: HistonesHistone
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2B
      • Protein or peptide: BJ4_G0007000.mRNA.1.CDS.1
      • Protein or peptide: Histone H2A
    • Complex: DNA (152-MER), DNA (123-MER)
      • DNA: DNA (152-MER)
      • DNA: DNA (123-MER)
Function / homology
Function and homology information


Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...Mif2, N-terminal / Kinetochore CENP-C fungal homologue, Mif2, N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / 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 / 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
MIF2 isoform 1 / CSE4 isoform 1 / Histone H2B / Histone H2A / Histone H4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsYan K / Yang J / Zhang Z / Barford D
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/6 United Kingdom
Cancer Research UKC576/A14109 United Kingdom
CitationJournal: To Be Published
Title: Cenp-A nucleosome in complex with Cenp-C
Authors: Yan K / Yang J / Zhang Z / Barford D
History
DepositionMay 25, 2021-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7on1
  • Surface level: 0.011
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7on1
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12993.png

Downloads & links

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Map

FileDownload / File: emd_12993.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.031082341 - 0.057323515
Average (Standard dev.)0.00010721267 (±0.0014586484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z272.000272.000272.000
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0310.0570.000

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Supplemental data

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Sample components

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Entire : Cenp-A nucleosome in complex with Cenp-C

EntireName: Cenp-A nucleosome in complex with Cenp-C
Components
  • Complex: Cenp-A nucleosome in complex with Cenp-C
    • Complex: Kinetochore subunit
      • Protein or peptide: BJ4_G0006610.mRNA.1.CDS.1
    • Complex: HistonesHistone
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2B
      • Protein or peptide: BJ4_G0007000.mRNA.1.CDS.1
      • Protein or peptide: Histone H2A
    • Complex: DNA (152-MER), DNA (123-MER)
      • DNA: DNA (152-MER)
      • DNA: DNA (123-MER)

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Supramolecule #1: Cenp-A nucleosome in complex with Cenp-C

SupramoleculeName: Cenp-A nucleosome in complex with Cenp-C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Kinetochore subunit

SupramoleculeName: Kinetochore subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: unidentified baculovirus

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Supramolecule #3: Histones

SupramoleculeName: Histones / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: DNA (152-MER), DNA (123-MER)

SupramoleculeName: DNA (152-MER), DNA (123-MER) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: BJ4_G0006610.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0006610.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 62.553461 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MDYMKLGLKS RKTGIDVKQD IPKDEYSMEN IDDFFKDDET SLISMRRKSR RKSSLFLPST LNGDTKNVLP PFLQSYKSQD DEVVQSPSG KGDGSRRSSL LSHQSNFLSP ANDFEPIEEE PEQEENDIRG NDFATPITQK LSKPTYKRKY STRYSLDTSE S PSVRLTPD ...String:
MDYMKLGLKS RKTGIDVKQD IPKDEYSMEN IDDFFKDDET SLISMRRKSR RKSSLFLPST LNGDTKNVLP PFLQSYKSQD DEVVQSPSG KGDGSRRSSL LSHQSNFLSP ANDFEPIEEE PEQEENDIRG NDFATPITQK LSKPTYKRKY STRYSLDTSE S PSVRLTPD RITNKNVYSD VPDLVADEDD DDRVNTSLNT SDNALLEDEL EDDGFIPESE EDGDYIESDS SLDSGSDSAS DS DGDNTYQ EVEEEAEVNT NDNEDDYIRR QASDVVRTDS IIDRNGLRKS TRVKVAPLQY WRNEKIVYKR KSNKPVLDID KIV TYDESE DEEEILAAQR RKKQKKKPTP TRPYNYVPTG RPRGRPKKDP NAKENLIPED PNEDIIERIE SGGIENGEWL KHGI LEANV KISDTKEETK DEIIAFAPNL SQTEQVKDTK DENFALEIMF DKHKEYFASG ILKLPAISGQ KKLSNSFRTY ITFHV IQGI VEVTVCKNKF LSVKGSTFQI PAFNEYAIAN RGNDEAKMFF VQVTVSEDAN DDNDKELDST FDTFG

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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: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 11.52352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMSGRGKGG KGLGKGGAKR HRKILRDNIQ GITKPAIRRL ARRGGVKRIS GLIYEEVRAV LKSFLESVIR DSVTYTEHAK RKTVTSLDV VYALKRQGRT LYGFGG

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Macromolecule #3: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.408493 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMSAKAEKK PASKAPAEKK PAAKKTSTST DGKKRSKARK ETYSSYIYKV LKQTHPDTGI SQKSMSILNS FVNDIFERIA TEASKLAAY NKKSTISARE IQTAVRLILP GELAKHAVSE GTRAVTKYSS STQA

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Macromolecule #4: BJ4_G0007000.mRNA.1.CDS.1

MacromoleculeName: BJ4_G0007000.mRNA.1.CDS.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 27.013564 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMSSKQQWV SSAIQSDSSG RSLSNVNRLA GDQQSINDRA LSLLQRTRAT KNLFPRREER RRYESSKSDL DIETDYEDQA GNLEIETEN EEEAEMETEV PAPVRTHSYA LDRYVRQKRR EKQRKQSLKR VEKKYTPSEL ALYEIRKYQR STDLLISKIP F ARLVKEVT ...String:
GAMSSKQQWV SSAIQSDSSG RSLSNVNRLA GDQQSINDRA LSLLQRTRAT KNLFPRREER RRYESSKSDL DIETDYEDQA GNLEIETEN EEEAEMETEV PAPVRTHSYA LDRYVRQKRR EKQRKQSLKR VEKKYTPSEL ALYEIRKYQR STDLLISKIP F ARLVKEVT DEFTTKDQDL RWQSMAIMAL QEASEAYLVG LLEHTNLLAL HAKRITIMKK DMQLARRIRG QFI

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Macromolecule #5: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 14.141307 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMSGGKGGK AGSAAKASQS RSAKAGLTFP VGRVHRLLRR GNYAQRIGSG APVYLTAVLE YLAAEILELA GNAARDNKKT RIIPRHLQL AIRNDDELNK LLGNVTIAQG GVLPNIHQNL LPKKSAKATK ASQEL

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Macromolecule #6: DNA (152-MER)

MacromoleculeName: DNA (152-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.13877 KDa
SequenceString: (DA)(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) ...String:
(DA)(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)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DG)(DA)(DT)

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Macromolecule #7: DNA (123-MER)

MacromoleculeName: DNA (123-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 38.125273 KDa
SequenceString: (DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (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) ...String:
(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (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)

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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: 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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 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: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124953

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