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- EMDB-6942: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 36... -

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Basic information

Entry
Database: EMDB / ID: 6942
TitleSaccharomyces Cerevisiae Origin Recognition Complex Bound to a 36-bp Origin DNA containing ACS and B1 element
Map data
SampleOrigin Recognition Complex Bound to a 36-bp Essential Elements of ARS DNA:
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsLi N / Lam WH / Zhai Y / Cheng J / Cheng E / Zhao Y / Gao N / Tye BK
CitationJournal: Nature / Year: 2018
Title: Structure of the origin recognition complex bound to DNA replication origin.
Authors: Ningning Li / Wai Hei Lam / Yuanliang Zhai / Jiaxuan Cheng / Erchao Cheng / Yongqian Zhao / Ning Gao / Bik-Kwoon Tye
DateDeposition: Apr 21, 2018 / Header (metadata) release: Jul 11, 2018 / Map release: Jul 11, 2018 / Last update: Jul 11, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6942.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.05 Å/pix.
= 252.48 Å
240 pix
1.05 Å/pix.
= 252.48 Å
240 pix
1.05 Å/pix.
= 252.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.052 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.1459123 - 0.24654093
Average (Standard dev.)0.00068327424 (0.00735301)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.0.0.
Limit239.239.239.
Spacing240240240
CellA=B=C: 252.48001 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0521.0521.052
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z252.480252.480252.480
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.1460.2470.001

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Supplemental data

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Sample components

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Entire Origin Recognition Complex Bound to a 36-bp Essential Elements of...

EntireName: Origin Recognition Complex Bound to a 36-bp Essential Elements of ARS DNA
Details: Origin Recognition Complex (Orc1-6, chain A-F) Bound to a 36-bp Essential Elements of ARS DNA (a 36-bp dsDNA chain G-H)
Number of components: 1

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Component #1: protein, Origin Recognition Complex Bound to a 36-bp Essential El...

ProteinName: Origin Recognition Complex Bound to a 36-bp Essential Elements of ARS DNA
Details: Origin Recognition Complex (Orc1-6, chain A-F) Bound to a 36-bp Essential Elements of ARS DNA (a 36-bp dsDNA chain G-H)
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE

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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: 52.3 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 102000
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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