[English] 日本語
Yorodumi
- EMDB-1832: Drosophila melanogaster CMG complex bound to ADP.BeF3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1832
TitleDrosophila melanogaster CMG complex bound to ADP.BeF3
Map dataVolume file of the ADP.BeF3-bound CMG complex
Sample
  • Sample: Drosophila melanogaster CMG complex bound to ADP.BeF3
  • Protein or peptide: x 11 types
KeywordsAAA+ ATPase / Helicase / DNA replication
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / Resolution: 28.0 Å
AuthorsCosta A / Ilves I / Tamberg N / Petojevic T / Nogales E / Botchan MR / Berger JM
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: The structural basis for MCM2-7 helicase activation by GINS and Cdc45.
Authors: Alessandro Costa / Ivar Ilves / Nele Tamberg / Tatjana Petojevic / Eva Nogales / Michael R Botchan / James M Berger /
Abstract: Two central steps for initiating eukaryotic DNA replication involve loading of the Mcm2-7 helicase onto double-stranded DNA and its activation by GINS-Cdc45. To better understand these events, we ...Two central steps for initiating eukaryotic DNA replication involve loading of the Mcm2-7 helicase onto double-stranded DNA and its activation by GINS-Cdc45. To better understand these events, we determined the structures of Mcm2-7 and the CMG complex by using single-particle electron microscopy. Mcm2-7 adopts two conformations--a lock-washer-shaped spiral state and a planar, gapped-ring form--in which Mcm2 and Mcm5 flank a breach in the helicase perimeter. GINS and Cdc45 bridge this gap, forming a topologically closed assembly with a large interior channel; nucleotide binding further seals off the discontinuity between Mcm2 and Mcm5, partitioning the channel into two smaller pores. Together, our data help explain how GINS and Cdc45 activate Mcm2-7, indicate that Mcm2-7 loading may be assisted by a natural predisposition of the hexamer to form open rings, and suggest a mechanism by which the CMG complex assists DNA strand separation.
History
DepositionNov 28, 2010-
Header (metadata) releaseDec 9, 2010-
Map releaseApr 8, 2011-
UpdateApr 8, 2011-
Current statusApr 8, 2011Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.42
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.42
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_1832.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume file of the ADP.BeF3-bound CMG complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.7 Å/pix.
x 64 pix.
= 364.8 Å
5.7 Å/pix.
x 64 pix.
= 364.8 Å
5.7 Å/pix.
x 64 pix.
= 364.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.7 Å
Density
Contour LevelBy AUTHOR: 0.42 / Movie #1: 0.42
Minimum - Maximum-0.15938 - 2.05233
Average (Standard dev.)-0.00245379 (±0.155001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 364.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.75.75.7
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z364.800364.800364.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-30-24-70
NX/NY/NZ6149141
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-0.1592.052-0.002

-
Supplemental data

-
Sample components

+
Entire : Drosophila melanogaster CMG complex bound to ADP.BeF3

EntireName: Drosophila melanogaster CMG complex bound to ADP.BeF3
Components
  • Sample: Drosophila melanogaster CMG complex bound to ADP.BeF3
  • 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: Psf1
  • Protein or peptide: Psf2
  • Protein or peptide: Psf3
  • Protein or peptide: Sld5
  • Protein or peptide: Cdc45

+
Supramolecule #1000: Drosophila melanogaster CMG complex bound to ADP.BeF3

SupramoleculeName: Drosophila melanogaster CMG complex bound to ADP.BeF3 / type: sample / ID: 1000 / Details: The sample was monodisperse
Oligomeric state: One Mcm2-7 heterohexamer binds to one GINS heterotetramer and a Cdc45 monomer
Number unique components: 11
Molecular weightTheoretical: 700 KDa

+
Macromolecule #1: Mcm2

MacromoleculeName: Mcm2 / type: protein_or_peptide / ID: 1 / Name.synonym: Mcm2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 100 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #2: Mcm3

MacromoleculeName: Mcm3 / type: protein_or_peptide / ID: 2 / Name.synonym: Mcm3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 91 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #3: Mcm4

MacromoleculeName: Mcm4 / type: protein_or_peptide / ID: 3 / Name.synonym: Mcm4 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 97 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #4: Mcm5

MacromoleculeName: Mcm5 / type: protein_or_peptide / ID: 4 / Name.synonym: Mcm5 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 82 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #5: Mcm6

MacromoleculeName: Mcm6 / type: protein_or_peptide / ID: 5 / Name.synonym: Mcm6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 92 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #6: Mcm7

MacromoleculeName: Mcm7 / type: protein_or_peptide / ID: 6 / Name.synonym: Mcm7 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 81 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #7: Psf1

MacromoleculeName: Psf1 / type: protein_or_peptide / ID: 7 / Name.synonym: Psf1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 23 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #8: Psf2

MacromoleculeName: Psf2 / type: protein_or_peptide / ID: 8 / Name.synonym: Psf2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 23 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #9: Psf3

MacromoleculeName: Psf3 / type: protein_or_peptide / ID: 9 / Name.synonym: Psf3 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 25 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #10: Sld5

MacromoleculeName: Sld5 / type: protein_or_peptide / ID: 10 / Name.synonym: Sld5 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 26 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

+
Macromolecule #11: Cdc45

MacromoleculeName: Cdc45 / type: protein_or_peptide / ID: 11 / Name.synonym: Cdc45 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit Fly / Cell: Baculovirus infected insect cells / Location in cell: Nucleus
Molecular weightExperimental: 66 KDa
Recombinant expressionOrganism: Baculovirus infected insect cells

-
Experimental details

-
Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 30000
Sample stageSpecimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN / Average electron dose: 20 e/Å2 / Bits/pixel: 8

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider

+
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