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- EMDB-7293: Cryo-EM structure of CENP-A nucleosome in complex with kinetochor... -

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Basic information

Entry
Database: EMDB / ID: 7293
TitleCryo-EM structure of CENP-A nucleosome in complex with kinetochore protein CENP-N
SampleCentromeric nucleosome in complex with kinetochore protein CENP-N
SourceHomo sapiens / human
Map dataCryo-EM density map of CENP-A nucleosome in complex with kinetochore protein CENP-N
Methodsingle particle reconstruction, at 3.92 Å resolution
AuthorsChittori S / Hong J
CitationScience, 2017

Science, 2017 Yorodumi Papers
Structural mechanisms of centromeric nucleosome recognition by the kinetochore protein CENP-N.
Sagar Chittori / Jingjun Hong / Hayden Saunders / Hanqiao Feng / Rodolfo Ghirlando / Alexander E Kelly / Yawen Bai / Sriram Subramaniam

Validation ReportPDB-ID: 6buz

SummaryFull reportAbout validation report
DateDeposition: Dec 11, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Dec 20, 2017 / Last update: Jan 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0014
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0014
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6buz
  • Surface level: 0.0014
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_7293.map.gz (map file in CCP4 format, 702465 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
560 pix
0.42 Å/pix.
= 235.2 Å
560 pix
0.42 Å/pix.
= 235.2 Å
560 pix
0.42 Å/pix.
= 235.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.42 Å
Density
Contour Level:0.0014 (by author), 0.0014 (movie #1):
Minimum - Maximum-0.0023961891 - 0.0057761674
Average (Standard dev.)4.2810665E-5 (0.00027144956)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions560560560
Origin000
Limit559559559
Spacing560560560
CellA=B=C: 235.2 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.420.420.42
M x/y/z560560560
origin x/y/z0.0000.0000.000
length x/y/z235.200235.200235.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS560560560
D min/max/mean-0.0020.0060.000

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Supplemental data

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Sample components

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Entire Centromeric nucleosome in complex with kinetochore protein CENP-N

EntireName: Centromeric nucleosome in complex with kinetochore protein CENP-N
Number of components: 8

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Component #1: protein, Centromeric nucleosome in complex with kinetochore prote...

ProteinName: Centromeric nucleosome in complex with kinetochore protein CENP-N
Recombinant expression: No
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Histone H3-like centromeric protein A

ProteinName: Histone H3-like centromeric protein A / Recombinant expression: No
MassTheoretical: 18.195002 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #3: protein, Histone H4

ProteinName: Histone H4 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #4: protein, Histone H2A

ProteinName: Histone H2A / Recombinant expression: No
MassTheoretical: 14.165551 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #5: protein, Histone H2B

ProteinName: Histone H2B / Recombinant expression: No
MassTheoretical: 13.935239 kDa
Source (engineered)Expression System: Homo sapiens / human

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Component #6: nucleic-acid, DNA (147-MER)

Nucleic-acidName: DNA (147-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(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)
MassTheoretical: 45.13877 kDa

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Component #7: nucleic-acid, DNA (147-MER)

Nucleic-acidName: DNA (147-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DT)(DC)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(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)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT)(DC)(DG)(DA)(DT)
MassTheoretical: 45.610043 kDa

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Component #8: protein, Maltose-binding periplasmic protein, Centromere protein ...

ProteinName: Maltose-binding periplasmic protein, Centromere protein N chimera
Recombinant expression: No
MassTheoretical: 75.607797 kDa
Source (engineered)Expression System: Homo sapiens / human

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.7 mg/ml / pH: 7.4
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 61749
3D reconstructionSoftware: RELION / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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