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- PDB-8eal: SsoMCM hexamer bound to Mg/ADP-BeFx and DNA. Class 1. Merged part... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8eal | |||||||||
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Title | SsoMCM hexamer bound to Mg/ADP-BeFx and DNA. Class 1. Merged particles from datasets with 3 different DNA entities | |||||||||
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![]() | REPLICATION / TRANSFERASE/DNA / Helicase / ATPase / TRANSFERASE-DNA complex | |||||||||
Function / homology | ![]() MCM complex / DNA duplex unwinding / helicase activity / single-stranded DNA binding / DNA replication / DNA helicase / ATP hydrolysis activity / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.34 Å | |||||||||
![]() | Meagher, M. / Myasnikov, A. / Enemark, E.J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Two Distinct Modes of DNA Binding by an MCM Helicase Enable DNA Translocation. Authors: Martin Meagher / Alexander Myasnikov / Eric J Enemark / ![]() Abstract: A six-subunit ATPase ring forms the central hub of the replication forks in all domains of life. This ring performs a helicase function to separate the two complementary DNA strands to be replicated ...A six-subunit ATPase ring forms the central hub of the replication forks in all domains of life. This ring performs a helicase function to separate the two complementary DNA strands to be replicated and drives the replication machinery along the DNA. Disruption of this helicase/ATPase ring is associated with genetic instability and diseases such as cancer. The helicase/ATPase rings of eukaryotes and archaea consist of six minichromosome maintenance (MCM) proteins. Prior structural studies have shown that MCM rings bind one encircled strand of DNA in a spiral staircase, suggesting that the ring pulls this strand of DNA through its central pore in a hand-over-hand mechanism where the subunit at the bottom of the staircase dissociates from DNA and re-binds DNA one step above the staircase. With high-resolution cryo-EM, we show that the MCM ring of the archaeal organism binds an encircled DNA strand in two different modes with different numbers of subunits engaged to DNA, illustrating a plausible mechanism for the alternating steps of DNA dissociation and re-association that occur during DNA translocation. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 694.6 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 94.9 KB | Display | |
Data in CIF | ![]() | 145.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27980MC ![]() 8eafC ![]() 8eagC ![]() 8eahC ![]() 8eaiC ![]() 8eajC ![]() 8eakC ![]() 8eamC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein / DNA chain , 2 types, 7 molecules ABCDEFX
#1: Protein | Mass: 68641.961 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: MCM, SSO0774 / Plasmid: pEE078.1 / Production host: ![]() ![]() #2: DNA chain | | Mass: 3605.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 31 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/08T.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/08T.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-08T / [[[( #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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 |
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Sample preparation
Component | Name: SsoMCM hexamer bound to Mg/ADP-BeFx and DNA. Class 2. Merged particles from datasets with 3 different DNA entities. Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm |
Image recording | Electron dose: 78 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Details: Initial CTF was calculated by cryoSPARC Patch CTF. CTF parameters were refined during final homogeneous refinement in cryoSPARC. Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Details: Particles were merged from 3 different datasets of complexes that differ in the specific DNA present. The particles for each individual set were selected in equivalent ways: Particles were ...Details: Particles were merged from 3 different datasets of complexes that differ in the specific DNA present. The particles for each individual set were selected in equivalent ways: Particles were selected from a subset of micrographs with cryoSPARC blob picker. 2D class averages were calculated, selected and used as templates with cryoSPARC template picker. | ||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.34 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3126671 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: Bond distance and angle restraints for a tetrahedral Zn2+ coordination were applied. Bond distance and angle restraints for a octahedral Mg2+ coordination were applied. | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6MII Pdb chain-ID: B / Accession code: 6MII / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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