+Open data
-Basic information
Entry | Database: PDB / ID: 7yox | ||||||
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Title | Cryo-EM structure of the N-terminal domain of hMCM8/9 and HROB | ||||||
Components |
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Keywords | HYDROLASE / MCM8/9 | ||||||
Function / homology | Function and homology information MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / CDC6 association with the ORC:origin complex / MutSalpha complex binding / E2F-enabled inhibition of pre-replication complex formation / female gamete generation ...MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / CDC6 association with the ORC:origin complex / MutSalpha complex binding / E2F-enabled inhibition of pre-replication complex formation / female gamete generation / Unwinding of DNA / MCM complex / DNA duplex unwinding / single-stranded DNA helicase activity / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / DNA helicase activity / protein localization to chromatin / double-strand break repair via homologous recombination / Orc1 removal from chromatin / chromosome / single-stranded DNA binding / DNA helicase / cell cycle / protein stabilization / DNA damage response / chromatin binding / protein-containing complex binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å | ||||||
Authors | Zheng, J.F. / Weng, Z.F. / Liu, Y.F. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yox.cif.gz | 309.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yox.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7yox.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yox_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 7yox_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7yox_validation.xml.gz | 64.4 KB | Display | |
Data in CIF | 7yox_validation.cif.gz | 93.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/7yox ftp://data.pdbj.org/pub/pdb/validation_reports/yo/7yox | HTTPS FTP |
-Related structure data
Related structure data | 33989MC 7w7pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 35482.418 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM8, C20orf154 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UJA3, DNA helicase #2: Protein | Mass: 31572.082 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MCM9, C6orf61, MCMDC1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NXL9, DNA helicase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Minichromosome maintenance 8 and 9 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 95257 / Symmetry type: POINT |
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |