[English] 日本語
Yorodumi
- EMDB-32346: Cryo-EM structure of gMCM8/9 helicase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32346
TitleCryo-EM structure of gMCM8/9 helicase
Map datacryo-EM structure of gMCM8/9 NTD
Sample
  • Complex: Minichromosome maintenance 8 and 9
    • Protein or peptide: DNA helicase MCM9
    • Protein or peptide: DNA helicase MCM8
KeywordsMCM8/9 / HYDROLASE
Function / homology
Function and homology information


Activation of ATR in response to replication stress / CDC6 association with the ORC:origin complex / Activation of the pre-replicative complex / Orc1 removal from chromatin / MCM8-MCM9 complex / MCM complex / helicase activity / double-strand break repair via homologous recombination / single-stranded DNA binding / DNA helicase ...Activation of ATR in response to replication stress / CDC6 association with the ORC:origin complex / Activation of the pre-replicative complex / Orc1 removal from chromatin / MCM8-MCM9 complex / MCM complex / helicase activity / double-strand break repair via homologous recombination / single-stranded DNA binding / DNA helicase / DNA damage response / ATP hydrolysis activity / ATP binding / nucleus
Similarity search - Function
: / MCM8 winged helix 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 ...: / MCM8 winged helix 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 / 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
DNA helicase MCM8 / DNA helicase MCM9
Similarity search - Component
Biological speciesGallus gallus (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsZheng JF / Weng ZF / Liu YF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530015 China
CitationJournal: Elife / Year: 2023
Title: Structural and mechanistic insights into the MCM8/9 helicase complex.
Authors: Zhuangfeng Weng / Jiefu Zheng / Yiyi Zhou / Zuer Lu / Yixi Wu / Dongyi Xu / Huanhuan Li / Huanhuan Liang / Yingfang Liu /
Abstract: MCM8 and MCM9 form a functional helicase complex (MCM8/9) that plays an essential role in DNA homologous recombination repair for DNA double-strand break. However, the structural characterization of ...MCM8 and MCM9 form a functional helicase complex (MCM8/9) that plays an essential role in DNA homologous recombination repair for DNA double-strand break. However, the structural characterization of MCM8/9 for DNA binding/unwinding remains unclear. Here, we report structures of the MCM8/9 complex using cryo-electron microscopy single particle analysis. The structures reveal that MCM8/9 is arranged into a heterohexamer through a threefold symmetry axis, creating a central channel that accommodates DNA. Multiple characteristic hairpins from the N-terminal oligosaccharide/oligonucleotide (OB) domains of MCM8/9 protrude into the central channel and serve to unwind the duplex DNA. When activated by HROB, the structure of MCM8/9's N-tier ring converts its symmetry from to with a conformational change that expands the MCM8/9's trimer interface. Moreover, our structural dynamic analyses revealed that the flexible C-tier ring exhibited rotary motions relative to the N-tier ring, which is required for the unwinding ability of MCM8/9. In summary, our structural and biochemistry study provides a basis for understanding the DNA unwinding mechanism of MCM8/9 helicase in homologous recombination.
History
DepositionDec 6, 2021-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32346.png

Downloads & links

-
Map

FileDownload / File: emd_32346.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM structure of gMCM8/9 NTD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.43287212 - 0.7642674
Average (Standard dev.)0.00041799556 (±0.01752547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Minichromosome maintenance 8 and 9

EntireName: Minichromosome maintenance 8 and 9
Components
  • Complex: Minichromosome maintenance 8 and 9
    • Protein or peptide: DNA helicase MCM9
    • Protein or peptide: DNA helicase MCM8

-
Supramolecule #1: Minichromosome maintenance 8 and 9

SupramoleculeName: Minichromosome maintenance 8 and 9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Gallus gallus (chicken)

-
Macromolecule #1: DNA helicase MCM9

MacromoleculeName: DNA helicase MCM9 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 30.774307 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MALRADQVSL IGQVFESYLL QHHRDDILGI LRQGDDEAHY PVLVDALTLF ETNMEIGEYF NAFPSQVLPI FDGALRRAAM AVLQAATPS PELRMKPNLH ARISGLPICP ELTREHIPKT RDVGHFLSVT GTVIRTSLVK VLEFERSYIC NKCKHVFVAK A DFEQYYAF ...String:
MALRADQVSL IGQVFESYLL QHHRDDILGI LRQGDDEAHY PVLVDALTLF ETNMEIGEYF NAFPSQVLPI FDGALRRAAM AVLQAATPS PELRMKPNLH ARISGLPICP ELTREHIPKT RDVGHFLSVT GTVIRTSLVK VLEFERSYIC NKCKHVFVAK A DFEQYYAF CRPSACLNEE GCNSTKFTCL SGTSSSPSSC RDYQEIKIQE QVQRLSVGSI PRCMVVVLED DLVDSCKSGD DI TVYGVVM QRWKPFHQDA RCDLELVLKA NYVKVN

UniProtKB: DNA helicase MCM9

-
Macromolecule #2: DNA helicase MCM8

MacromoleculeName: DNA helicase MCM8 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 34.714797 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: ASSRLVQSTL DQFIPYKGWK LYFSEAYADK SPFVQKTQAF EKFFMQRIEL YDKDEIERKG SILVDYKELI EDRELTKSIP NISTELRDM PQKILQCMGL AIHQVLTKDL ERHAAELQVQ EGLPLDGEPI INVPLIHARL YNYEPLTQLK NVRANCYGKY I ALRGTVVR ...String:
ASSRLVQSTL DQFIPYKGWK LYFSEAYADK SPFVQKTQAF EKFFMQRIEL YDKDEIERKG SILVDYKELI EDRELTKSIP NISTELRDM PQKILQCMGL AIHQVLTKDL ERHAAELQVQ EGLPLDGEPI INVPLIHARL YNYEPLTQLK NVRANCYGKY I ALRGTVVR VSNIKPLCTK LAFVCGTCGD VQSVPLPDGK YTLPTKCLVP ECRGRSFTPD RSSPLTATVD WQSVKVQELM SD DQREAGR IPRTIECELV QDLVDSCVPG DVVTITGVVK VSSTEEGASK NKNDKCVFLL YIEANSVSNS K

UniProtKB: DNA helicase MCM8

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dp3


Details: 7DP3 and 7DPD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: OTHER / Number images used: 190119
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7w7p:
Cryo-EM structure of gMCM8/9 helicase

+
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