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

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Basic information

Entry
Database: PDB / ID: 7w7p
TitleCryo-EM structure of gMCM8/9 helicase
Components
  • DNA helicase MCM8
  • DNA helicase MCM9
KeywordsHYDROLASE / MCM8/9
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsZheng, J.F. / Weng, Z.F. / Liu, Y.F.
Funding support China, 1items
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, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA helicase MCM9
B: DNA helicase MCM8
C: DNA helicase MCM9
D: DNA helicase MCM8
E: DNA helicase MCM9
F: DNA helicase MCM8


Theoretical massNumber of molelcules
Total (without water)196,4676
Polymers196,4676
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein DNA helicase MCM9 / Minichromosome maintenance 9


Mass: 30774.307 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MCM9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I0IUP4, DNA helicase
#2: Protein DNA helicase MCM8 / Minichromosome maintenance 8


Mass: 34714.797 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MCM8, RCJMB04_5o15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: I0IUP3, DNA helicase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Minichromosome maintenance 8 and 9 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Gallus gallus (chicken)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.67 Å / Resolution method: OTHER / Num. of particles: 190119 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00513428
ELECTRON MICROSCOPYf_angle_d0.66718199
ELECTRON MICROSCOPYf_dihedral_angle_d4.5291820
ELECTRON MICROSCOPYf_chiral_restr0.0452087
ELECTRON MICROSCOPYf_plane_restr0.0082354

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