[English] 日本語
Yorodumi
- EMDB-6671: Cryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6671
TitleCryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state
Map data
SampleCdt1-MCM2-7
  • (DNA replication licensing factor ...) x 5
  • Minichromosome maintenance protein 5
  • Cell division cycle protein CDT1Cell cycle
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Activation of the pre-replicative complex / Orc1 removal from chromatin / MCM complex binding / go:1902450: / MCM core complex / CMG complex / nuclear DNA replication / mitotic DNA replication / negative regulation of chromatin silencing at telomere ...Switching of origins to a post-replicative state / Activation of the pre-replicative complex / Orc1 removal from chromatin / MCM complex binding / go:1902450: / MCM core complex / CMG complex / nuclear DNA replication / mitotic DNA replication / negative regulation of chromatin silencing at telomere / establishment of chromatin silencing / MCM complex / regulation of DNA-dependent DNA replication initiation / nuclear pre-replicative complex / DNA replication preinitiation complex / go:0043142: / mitotic DNA replication initiation / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / double-strand break repair via break-induced replication / nuclear replication fork / replication fork protection complex / DNA strand elongation involved in DNA replication / chromatin silencing at silent mating-type cassette / DNA duplex unwinding / DNA unwinding involved in DNA replication / DNA replication origin binding / chromatin silencing at telomere / DNA replication initiation / DNA helicase activity / chromosome, telomeric region / DNA helicase / helicase activity / single-stranded DNA binding / nuclear chromosome, telomeric region / cell division / cellular response to DNA damage stimulus / chromatin binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Mcm6, C-terminal winged-helix domain / Mini-chromosome maintenance, conserved site / MCM, AAA-lid domain / MCM domain / AAA+ ATPase domain / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / MCM N-terminal domain / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm5 ...Mcm6, C-terminal winged-helix domain / Mini-chromosome maintenance, conserved site / MCM, AAA-lid domain / MCM domain / AAA+ ATPase domain / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm3 / MCM N-terminal domain / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mini-chromosome maintenance protein 2 / Nucleic acid-binding, OB-fold / MCM OB domain / MCM N-terminal domain / MCM OB domain / Mini-chromosome maintenance protein / P-loop containing nucleoside triphosphate hydrolase / MCM family domain profile. / MCM family signature. / MCM6 C-terminal winged-helix domain / MCM AAA-lid domain / MCM P-loop domain
DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / Cell division cycle protein CDT1 / DNA replication licensing factor MCM6
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsZhai Y / Cheng E / Wu H / Li N / Yung PY / Gao N / Tye BK
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Open-ringed structure of the Cdt1-Mcm2-7 complex as a precursor of the MCM double hexamer.
Authors: Yuanliang Zhai / Erchao Cheng / Hao Wu / Ningning Li / Philip Yuk Kwong Yung / Ning Gao / Bik-Kwoon Tye /
Abstract: The minichromosome maintenance complex (MCM) hexameric complex (Mcm2-7) forms the core of the eukaryotic replicative helicase. During G1 phase, two Cdt1-Mcm2-7 heptamers are loaded onto each ...The minichromosome maintenance complex (MCM) hexameric complex (Mcm2-7) forms the core of the eukaryotic replicative helicase. During G1 phase, two Cdt1-Mcm2-7 heptamers are loaded onto each replication origin by the origin-recognition complex (ORC) and Cdc6 to form an inactive MCM double hexamer (DH), but the detailed loading mechanism remains unclear. Here we examine the structures of the yeast MCM hexamer and Cdt1-MCM heptamer from Saccharomyces cerevisiae. Both complexes form left-handed coil structures with a 10-15-Å gap between Mcm5 and Mcm2, and a central channel that is occluded by the C-terminal domain winged-helix motif of Mcm5. Cdt1 wraps around the N-terminal regions of Mcm2, Mcm6 and Mcm4 to stabilize the whole complex. The intrinsic coiled structures of the precursors provide insights into the DH formation, and suggest a spring-action model for the MCM during the initial origin melting and the subsequent DNA unwinding.
Validation ReportPDB-ID: 5xf8

SummaryFull reportAbout validation report
History
DepositionNov 18, 2016-
Header (metadata) releaseJan 18, 2017-
Map releaseFeb 8, 2017-
UpdateMar 15, 2017-
Current statusMar 15, 2017Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0225
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0225
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5xf8
  • Surface level: 0.0225
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_6671.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 200 pix.
= 264. Å
1.32 Å/pix.
x 200 pix.
= 264. Å
1.32 Å/pix.
x 200 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.0253 / Movie #1: 0.0225
Minimum - Maximum-0.02483477 - 0.06754894
Average (Standard dev.)0.00018060292 (±0.0047354507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0250.0680.000

-
Supplemental data

-
Sample components

+
Entire Cdt1-MCM2-7

EntireName: Cdt1-MCM2-7 / Number of components: 8

+
Component #1: protein, Cdt1-MCM2-7

ProteinName: Cdt1-MCM2-7 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast) / Vector: yJF38

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

+
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)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

-
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: 22 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 63000
3D reconstructionResolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more