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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: EMD-6942
TitleSaccharomyces Cerevisiae Origin Recognition Complex Bound to a 36-bp Origin DNA containing ACS and B1 element
Map data
Sample
  • Complex: Origin Recognition Complex Bound to a 36-bp Essential Elements of ARS DNA
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
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 /
Abstract: The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the ...The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the Saccharomyces cerevisiae ORC bound to a 72-base-pair origin DNA sequence that contains the ARS consensus sequence (ACS) and the B1 element. The ORC encircles DNA through extensive interactions with both phosphate backbone and bases, and bends DNA at the ACS and B1 sites. Specific recognition of thymine residues in the ACS is carried out by a conserved basic amino acid motif of Orc1 in the minor groove, and by a species-specific helical insertion motif of Orc4 in the major groove. Moreover, similar insertions into major and minor grooves are also embedded in the B1 site by basic patch motifs from Orc2 and Orc5, respectively, to contact bases and to bend DNA. This work pinpoints a conserved role of ORC in modulating DNA structure to facilitate origin selection and helicase loading in eukaryotes.
History
DepositionApr 21, 2018-
Header (metadata) releaseJul 11, 2018-
Map releaseJul 11, 2018-
UpdateJul 25, 2018-
Current statusJul 25, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Supplemental images

emd_6942.png

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Map

FileDownload / File: emd_6942.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.1459123 - 0.24654093
Average (Standard dev.)0.00068327424 (±0.00735301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 252.48001 Å
α=β=γ: 90.0 °

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
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
Components
  • Complex: Origin Recognition Complex Bound to a 36-bp Essential Elements of ARS DNA

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Supramolecule #1: Origin Recognition Complex Bound to a 36-bp Essential Elements of...

SupramoleculeName: Origin Recognition Complex Bound to a 36-bp Essential Elements of ARS DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
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)
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)

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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: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 52.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 102000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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