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- EMDB-8540: Structural basis of MCM2-7 replicative helicase loading by ORC-Cd... -

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Basic information

Entry
Database: EMDB / ID: 8540
TitleStructural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1
Map dataTetrameric HIV-1 Strand Transfer Complex Intasome
SampleORC-Cdc6-Cdt1-MCM2-7
  • (DNA replication licensing factor ...) x 5
  • Minichromosome maintenance protein 5
  • (Cell division ...) x 2
  • (Origin recognition complex subunit ...) x 6
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homologyMini-chromosome maintenance complex protein 4 / Cdc6, C-terminal / Origin recognition complex subunit 6 (ORC6) / Bromo adjacent homology (BAH) domain / MCM domain / AAA+ ATPase domain / ATPase, AAA-type, core / Origin recognition complex, subunit 2 / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 ...Mini-chromosome maintenance complex protein 4 / Cdc6, C-terminal / Origin recognition complex subunit 6 (ORC6) / Bromo adjacent homology (BAH) domain / MCM domain / AAA+ ATPase domain / ATPase, AAA-type, core / Origin recognition complex, subunit 2 / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / Origin recognition complex subunit 2 / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Origin recognition complex, subunit 6 / Nucleic acid-binding, OB-fold / Cell division protein Cdc6/18 / BAH domain / Origin recognition complex subunit 4 / Origin recognition complex, subunit 6, fungi / Mini-chromosome maintenance, conserved site / Origin recognition complex, subunit 1 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / P-loop containing nucleoside triphosphate hydrolase / MCM N-terminal domain / Mini-chromosome maintenance protein / Origin recognition complex subunit 4, C-terminal / MCM OB domain / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / ATPase family associated with various cellular activities (AAA) / CDC6, C terminal winged helix domain / MCM P-loop domain / Orc1 removal from chromatin / Mini-chromosome maintenance protein 2 / CDK-mediated phosphorylation and removal of Cdc6 / CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / BAH domain profile. / MCM family domain profile. / MCM family signature. / MCM OB domain / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / MCM N-terminal domain / Activation of the pre-replicative complex / AAA domain / Switching of origins to a post-replicative state / nuclear origin of replication recognition complex / MCM core complex / MCM complex binding / negative regulation of ATP-dependent DNA helicase activity / CMG complex / nuclear DNA replication / regulation of chromatin silencing at telomere / negative regulation of chromatin silencing at telomere / MCM complex / establishment of chromatin silencing / mitotic DNA replication initiation / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / DNA replication preinitiation complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / single-stranded DNA-dependent ATPase activity / mitotic DNA replication checkpoint / double-strand break repair via break-induced replication / nuclear replication fork / DNA strand elongation involved in DNA replication / replication fork protection complex / chromatin silencing at silent mating-type cassette / histone H3-K4 methylation / DNA duplex unwinding / DNA helicase activity / DNA unwinding involved in DNA replication / chromatin silencing at telomere / DNA replication origin binding / DNA replication initiation / DNA helicase / helicase activity / chromosome, telomeric region / G1/S transition of mitotic cell cycle / single-stranded DNA binding / chromosome / mitotic cell cycle / nuclear chromosome, telomeric region / ATPase activity / GTPase activity / cell division / GTP binding / cellular response to DNA damage stimulus / chromatin binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / Origin recognition complex subunit 6 / Origin recognition complex subunit 3 / Origin recognition complex subunit 1
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsYuan Z / Riera A / Bai L / Sun J / Spanos C / Chen ZA / Barbon M / Rappsilber J / Stillman B / Speck C / Li H
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1.
Authors: Zuanning Yuan / Alberto Riera / Lin Bai / Jingchuan Sun / Saikat Nandi / Christos Spanos / Zhuo Angel Chen / Marta Barbon / Juri Rappsilber / Bruce Stillman / Christian Speck / Huilin Li
Validation ReportPDB-ID: 5v8f

SummaryFull reportAbout validation report
DateDeposition: Dec 25, 2016 / Header (metadata) release: Feb 22, 2017 / Map release: Feb 22, 2017 / Last update: Nov 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5v8f
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5v8f
  • Surface level: 0.021
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8540.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
256 pix
1.01 Å/pix.
= 258.56 Å
256 pix
1.01 Å/pix.
= 258.56 Å
256 pix
1.01 Å/pix.
= 258.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.01 Å
Density
Contour Level:0.021 (by author), 0.021 (movie #1):
Minimum - Maximum-0.03851721 - 0.10812734
Average (Standard dev.)0.0004973546 (0.004821395)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderZYX
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 258.56 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.011.011.01
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z258.560258.560258.560
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0390.1080.000

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Supplemental data

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Sample components

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Entire ORC-Cdc6-Cdt1-MCM2-7

EntireName: ORC-Cdc6-Cdt1-MCM2-7 / Number of components: 18

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Component #1: protein, ORC-Cdc6-Cdt1-MCM2-7

ProteinName: ORC-Cdc6-Cdt1-MCM2-7 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: pRS

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Component #2: protein, DNA replication licensing factor MCM2

ProteinName: DNA replication licensing factor MCM2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.911539 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, DNA replication licensing factor MCM3

ProteinName: DNA replication licensing factor MCM3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 107.653508 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, DNA replication licensing factor MCM4

ProteinName: DNA replication licensing factor MCM4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.138375 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, Minichromosome maintenance protein 5

ProteinName: Minichromosome maintenance protein 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.505734 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, DNA replication licensing factor MCM6

ProteinName: DNA replication licensing factor MCM6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 113.110211 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, DNA replication licensing factor MCM7

ProteinName: DNA replication licensing factor MCM7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 95.049875 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: protein, Cell division cycle protein CDT1

ProteinName: Cell division cycle protein CDT1Cell cycle / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 68.486055 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 #9: protein, Cell division control protein 6

ProteinName: Cell division control protein 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.112367 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 #10: 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 #11: 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 #12: 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 #13: 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 #14: 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 #15: 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 #16: nucleic-acid, DNA (39-MER)

Nucleic-acidName: DNA (39-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DA)(DT)(DT)(DT)(DA)(DA)(DG)(DT)(DA) (DT)(DT)(DG)(DT)(DT)(DT)(DG)(DT)(DG)(DC) (DA)(DC)(DT)(DT)(DG)(DC)(DC)(DT)(DG)(DC) (DA)(DG)(DG)(DC)(DC)(DT)(DT)(DT)(DT)
MassTheoretical: 11.967674 kDa
SourceSpecies: synthetic construct (others)

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Component #17: nucleic-acid, DNA (39-MER)

Nucleic-acidName: DNA (39-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DA)(DA)(DA)(DA)(DG)(DG)(DC)(DC)(DT)(DG) (DC)(DA)(DG)(DG)(DC)(DA)(DA)(DG)(DT)(DG) (DC)(DA)(DC)(DA)(DA)(DA)(DC)(DA)(DA)(DT) (DA)(DC)(DT)(DT)(DA)(DA)(DA)(DT)(DA)
MassTheoretical: 12.035815 kDa
SourceSpecies: synthetic construct (others)

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Component #18: ligand, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

LigandName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 0.523247 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 304288
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Output model

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