[English] 日本語
Yorodumi
- EMDB-3321: CryoEM structure of the ATP-treated CMG replicative helicase (rel... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3321
TitleCryoEM structure of the ATP-treated CMG replicative helicase (relaxed state)
Map dataCMG treated with ATP showing a loose Mcm5-2 AAA+ configuration
Sample
  • Sample: CMG treated with ATP
  • Protein or peptide: x 11 types
KeywordsCdc45 / GINS / MCM / CMG / helicase / DNA replication
Function / homology
Function and homology information


Unwinding of DNA / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / DNA endoreduplication / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / DNA strand elongation involved in mitotic DNA replication ...Unwinding of DNA / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / DNA endoreduplication / Activation of ATR in response to replication stress / Activation of the pre-replicative complex / eggshell chorion gene amplification / Orc1 removal from chromatin / DNA amplification / DNA strand elongation involved in mitotic DNA replication / GINS complex / mitotic DNA replication preinitiation complex assembly / resolution of meiotic recombination intermediates / premeiotic DNA replication / mitotic DNA replication / CMG complex / DNA replication preinitiation complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / chromosome condensation / DNA strand elongation involved in DNA replication / DNA replication origin binding / DNA replication initiation / regulation of DNA-templated transcription elongation / mitotic spindle organization / meiotic cell cycle / mitotic cell cycle / single-stranded DNA binding / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / cell division / chromatin binding / ATP hydrolysis activity / zinc ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA replication licensing factor MCM2-like, winged-helix domain / : / PSF3 N-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 / GINS complex, subunit Psf3 / GINS complex, subunit Psf1 ...DNA replication licensing factor MCM2-like, winged-helix domain / : / PSF3 N-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 / GINS complex, subunit Psf3 / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / GINS complex, subunit Psf3 superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS complex subunit Sld5 / GINS subunit, domain A / GINS subunit, domain A / GINS complex protein helical bundle domain / MCM4, winged helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm5 / MCM3-like, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CDC45L / DNA replication licensing factor Mcm2 / DNA replication licensing factor MCM4 / DNA replication licensing factor Mcm6 / DNA replication complex GINS protein SLD5 / DNA replication licensing factor Mcm5 / Probable DNA replication complex GINS protein PSF2 / DNA replication complex GINS protein PSF1 / DNA replication complex GINS protein PSF3 / DNA replication licensing factor Mcm7 / DNA replication licensing factor Mcm3
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsRenault L / Costa A
CitationJournal: Nat Commun / Year: 2016
Title: Cryo-EM structures of the eukaryotic replicative helicase bound to a translocation substrate.
Authors: Ferdos Abid Ali / Ludovic Renault / Julian Gannon / Hailey L Gahlon / Abhay Kotecha / Jin Chuan Zhou / David Rueda / Alessandro Costa /
Abstract: The Cdc45-MCM-GINS (CMG) helicase unwinds DNA during the elongation step of eukaryotic genome duplication and this process depends on the MCM ATPase function. Whether CMG translocation occurs on ...The Cdc45-MCM-GINS (CMG) helicase unwinds DNA during the elongation step of eukaryotic genome duplication and this process depends on the MCM ATPase function. Whether CMG translocation occurs on single- or double-stranded DNA and how ATP hydrolysis drives DNA unwinding remain open questions. Here we use cryo-electron microscopy to describe two subnanometre resolution structures of the CMG helicase trapped on a DNA fork. In the predominant state, the ring-shaped C-terminal ATPase of MCM is compact and contacts single-stranded DNA, via a set of pre-sensor 1 hairpins that spiral around the translocation substrate. In the second state, the ATPase module is relaxed and apparently substrate free, while DNA intimately contacts the downstream amino-terminal tier of the MCM motor ring. These results, supported by single-molecule FRET measurements, lead us to suggest a replication fork unwinding mechanism whereby the N-terminal and AAA+ tiers of the MCM work in concert to translocate on single-stranded DNA.
History
DepositionFeb 1, 2016-
Header (metadata) releaseFeb 10, 2016-
Map releaseFeb 24, 2016-
UpdateFeb 8, 2017-
Current statusFeb 8, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3321.png

Downloads & links

-
Map

FileDownload / File: emd_3321.map.gz / Format: CCP4 / Size: 17.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCMG treated with ATP showing a loose Mcm5-2 AAA+ configuration
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 168 pix.
= 297.36 Å		1.77 Å/pix.
x 168 pix.
= 297.36 Å		1.77 Å/pix.
x 168 pix.
= 297.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.19081141 - 0.30471283
Average (Standard dev.)0.00326462 (±0.01997862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z297.360297.360297.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.1910.3050.003

-
Supplemental data

-
Sample components

+
Entire : CMG treated with ATP

EntireName: CMG treated with ATP
Components
  • Sample: CMG treated with ATP
  • Protein or peptide: Mcm2
  • Protein or peptide: Mcm3
  • Protein or peptide: Mcm4
  • Protein or peptide: Mcm5
  • Protein or peptide: Mcm6
  • Protein or peptide: Mcm7
  • Protein or peptide: Cdc45
  • Protein or peptide: Psf1
  • Protein or peptide: Psf2
  • Protein or peptide: Psf3
  • Protein or peptide: Sld5

+
Supramolecule #1000: CMG treated with ATP

SupramoleculeName: CMG treated with ATP / type: sample / ID: 1000 / Number unique components: 11
Molecular weightExperimental: 700 KDa / Theoretical: 700 KDa

+
Macromolecule #1: Mcm2

MacromoleculeName: Mcm2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 100 KDa / Theoretical: 100 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Mcm2
SequenceUniProtKB: DNA replication licensing factor Mcm2 / InterPro: DNA replication licensing factor Mcm2

+
Macromolecule #2: Mcm3

MacromoleculeName: Mcm3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 90 KDa / Theoretical: 90 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Mcm3
SequenceUniProtKB: DNA replication licensing factor Mcm3 / InterPro: DNA replication licensing factor Mcm3

+
Macromolecule #3: Mcm4

MacromoleculeName: Mcm4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 97 KDa / Theoretical: 97 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Mcm4
SequenceUniProtKB: DNA replication licensing factor MCM4 / InterPro: Mini-chromosome maintenance complex protein 4

+
Macromolecule #4: Mcm5

MacromoleculeName: Mcm5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 82 KDa / Theoretical: 82 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Mcm5
SequenceUniProtKB: DNA replication licensing factor Mcm5 / InterPro: DNA replication licensing factor Mcm5

+
Macromolecule #5: Mcm6

MacromoleculeName: Mcm6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 92 KDa / Theoretical: 92 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Mcm6
SequenceUniProtKB: DNA replication licensing factor Mcm6 / InterPro: DNA replication licensing factor Mcm6

+
Macromolecule #6: Mcm7

MacromoleculeName: Mcm7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 81 KDa / Theoretical: 81 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Mcm7
SequenceUniProtKB: DNA replication licensing factor Mcm7 / InterPro: DNA replication licensing factor Mcm7

+
Macromolecule #7: Cdc45

MacromoleculeName: Cdc45 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 66 KDa / Theoretical: 66 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-cdc45
SequenceUniProtKB: CDC45L / InterPro: CDC45 family

+
Macromolecule #8: Psf1

MacromoleculeName: Psf1 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 23 KDa / Theoretical: 23 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Psf1
SequenceUniProtKB: DNA replication complex GINS protein PSF1 / InterPro: GINS subunit, domain A

+
Macromolecule #9: Psf2

MacromoleculeName: Psf2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 23 KDa / Theoretical: 23 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Psf2
SequenceUniProtKB: Probable DNA replication complex GINS protein PSF2
InterPro: DNA replication complex GINS protein Psf2

+
Macromolecule #10: Psf3

MacromoleculeName: Psf3 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Psf3
SequenceUniProtKB: DNA replication complex GINS protein PSF3 / InterPro: GINS complex, subunit Psf3

+
Macromolecule #11: Sld5

MacromoleculeName: Sld5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly
Molecular weightExperimental: 26 KDa / Theoretical: 26 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastBac-Sld5
SequenceUniProtKB: DNA replication complex GINS protein SLD5 / InterPro: GINS complex subunit Sld5

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
Details: 25 mM Hepes, 50 mM sodium acetate, 10 mM magnesium acetate, 1 mM DTT, 1mM ATP
GridDetails: 400 mesh quantifoils 1.2/1.3 open holes
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 5 seconds before plunging

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DateDec 4, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Number real images: 536 / Average electron dose: 51 e/Å2 / Details: data was recorded as movies of 51 frames / Bits/pixel: 32
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsParticles were picked in Xmipp 3.0; Contrast Transfer Function was estimated using CTFFIND3. All further processing was performed within the RELION 1.3 environment.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: OTHER / Software - Name: RELION1.3 / Number images used: 13182
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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