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- EMDB-32346: Cryo-EM structure of gMCM8/9 helicase -

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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 / DNA duplex unwinding / helicase activity / double-strand break repair via homologous recombination / single-stranded DNA binding ...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 / DNA duplex unwinding / 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
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 / ATPases associated with a variety of cellular activities ...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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / 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-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32346.png

Downloads & links

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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
Voxel sizeX=Y=Z: 1 Å
Density
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 °

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Supplemental data

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Sample components

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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

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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)

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

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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

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Image processing

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

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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