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- EMDB-6941: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72... -

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Basic information

Entry
Database: EMDB / ID: 6941
TitleSaccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Map data
SampleSaccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
  • (Origin recognition complex subunit ...) x 6
  • (nucleic-acidNucleic acid) x 2
  • (ligand) x 2
Function / homologyOrigin recognition complex, subunit 1 / ATPase, AAA-type, core / AAA domain / Origin recognition complex subunit 6 (ORC6) / Origin recognition complex subunit 2 / BAH domain / ATPase family associated with various cellular activities (AAA) / Origin recognition complex subunit 4, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Origin recognition complex, subunit 5 ...Origin recognition complex, subunit 1 / ATPase, AAA-type, core / AAA domain / Origin recognition complex subunit 6 (ORC6) / Origin recognition complex subunit 2 / BAH domain / ATPase family associated with various cellular activities (AAA) / Origin recognition complex subunit 4, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Origin recognition complex, subunit 5 / Origin recognition complex, subunit 3 / BAH domain profile. / Origin recognition complex, subunit 6, fungi / Origin recognition complex subunit 4 / Origin recognition complex, subunit 6 / Origin recognition complex, subunit 2 / AAA+ ATPase domain / Origin recognition complex (ORC) subunit 5 C-terminus / Bromo adjacent homology (BAH) domain / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / Activation of the pre-replicative complex / Origin recognition complex (ORC) subunit 4 C-terminus / regulation of chromatin silencing at telomere / nuclear origin of replication recognition complex / nuclear pre-replicative complex / DNA replication preinitiation complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / chromatin silencing at silent mating-type cassette / histone H3-K4 methylation / chromatin silencing at telomere / DNA replication origin binding / DNA replication initiation / chromosome, telomeric region / ATPase activity / chromatin binding / ATP binding / nucleus / Origin recognition complex subunit 2 / Origin recognition complex subunit 6 / Origin recognition complex subunit 5 / Origin recognition complex subunit 1 / Origin recognition complex subunit 3 / Origin recognition complex subunit 4
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 3 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
Validation ReportPDB-ID: 5zr1

SummaryFull reportAbout validation report
DateDeposition: Apr 21, 2018 / Header (metadata) release: Jul 11, 2018 / Map release: Jul 11, 2018 / Last update: Jul 25, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5zr1
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6941.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.05 Å/pix.
= 269.312 Å
256 pix
1.05 Å/pix.
= 269.312 Å
256 pix
1.05 Å/pix.
= 269.312 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:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.19995214 - 0.44266602
Average (Standard dev.)0.0006592716 (0.010016402)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.0.0.
Limit255.255.255.
Spacing256256256
CellA=B=C: 269.312 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/z256256256
origin x/y/z0.0000.0000.000
length x/y/z269.312269.312269.312
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.2000.4430.001

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Supplemental data

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Sample components

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Entire Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72...

EntireName: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Details: Saccharomyces Cerevisiae Origin Recognition Complex (Orc1-6, chain A-F) Bound to a 72-bp Origin DNA (a 72-bp dsDNA chain G-H) containing ACS and B1 element
Number of components: 11

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Component #1: protein, Saccharomyces Cerevisiae Origin Recognition Complex Boun...

ProteinName: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Details: Saccharomyces Cerevisiae Origin Recognition Complex (Orc1-6, chain A-F) Bound to a 72-bp Origin DNA (a 72-bp dsDNA chain G-H) containing ACS and B1 element
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Origin recognition complex subunit 1

ProteinName: Origin recognition complex subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.546164 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #3: protein, Origin recognition complex subunit 2

ProteinName: Origin recognition complex subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 71.34218 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #4: protein, Origin recognition complex subunit 3

ProteinName: Origin recognition complex subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.161766 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #5: protein, Origin recognition complex subunit 4

ProteinName: Origin recognition complex subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.772152 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #6: protein, Origin recognition complex subunit 5

ProteinName: Origin recognition complex subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.347168 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #7: protein, Origin recognition complex subunit 6

ProteinName: Origin recognition complex subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 50.369531 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)

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Component #8: nucleic-acid, 72bp-oring DNA, ACS305, T-rich

Nucleic-acidName: 72bp-oring DNA, ACS305, T-rich / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DT) (DA)(DT)(DG)(DT)(DT)(DT)(DT)(DG)(DT)(DT) (DA)(DT)(DG)(DT)(DA)(DT)(DT)(DG)(DT)(DT) (DT)(DA)(DT)(DT)(DT)(DT)(DC)(DC)(DC)(DT) (DT)(DT)(DA)(DA)(DT)(DT)(DT)(DT)(DA)(DG) (DG)(DA)(DT)(DA)(DT)(DG)(DA)(DA)(DA)(DA) (DC)(DA)(DA)(DG)(DA)(DA)(DT)(DT)(DT)(DA) (DT)(DC)
MassTheoretical: 22.203266 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #9: nucleic-acid, 72bp-oring DNA, ACS305, A-rich

Nucleic-acidName: 72bp-oring DNA, ACS305, A-rich / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DA)(DT)(DA)(DA)(DA)(DT)(DT)(DC)(DT) (DT)(DG)(DT)(DT)(DT)(DT)(DC)(DA)(DT)(DA) (DT)(DC)(DC)(DT)(DA)(DA)(DA)(DA)(DT)(DT) (DA)(DA)(DA)(DG)(DG)(DG)(DA)(DA)(DA)(DA) (DT)(DA)(DA)(DA)(DC)(DA)(DA)(DT)(DA)(DC) (DA)(DT)(DA)(DA)(DC)(DA)(DA)(DA)(DA)(DC) (DA)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DA)(DC) (DC)(DA)
MassTheoretical: 22.174412 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #10: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

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Component #11: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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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: 164857
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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