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- EMDB-27976: SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT. Class 1 -
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Open data
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Basic information
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Title | SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT. Class 1 | |||||||||
![]() | unsharpened map | |||||||||
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![]() | Helicase / ATPase / REPLICATION / 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.48 Å | |||||||||
![]() | Meagher M / Myasnikov A / Enemark EJ | |||||||||
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
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.7 KB 22.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 129.6 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.7 KB | ||
Others | ![]() ![]() ![]() | 59.7 MB 59.3 MB 59.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 779.7 KB | Display | ![]() |
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Full document | ![]() | 779.3 KB | Display | |
Data in XML | ![]() | 16 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eahMC ![]() 8eafC ![]() 8eagC ![]() 8eaiC ![]() 8eajC ![]() 8eakC ![]() 8ealC ![]() 8eamC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: sharpened map
File | emd_27976_additional_1.map | ||||||||||||
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Annotation | sharpened map | ||||||||||||
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-Half map: half-map B
File | emd_27976_half_map_1.map | ||||||||||||
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Annotation | half-map B | ||||||||||||
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-Half map: half-map A
File | emd_27976_half_map_2.map | ||||||||||||
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Annotation | half-map A | ||||||||||||
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Sample components
-Entire : SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT Class 1
Entire | Name: SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT Class 1 |
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Components |
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-Supramolecule #1: SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT Class 1
Supramolecule | Name: SsoMCM hexamer bound to Mg/ADP-BeFx and 16-mer oligo-dT Class 1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Minichromosome maintenance protein MCM
Macromolecule | Name: Minichromosome maintenance protein MCM / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: DNA helicase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 68.641961 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: SLEIPSKQID YRDVFIEFLT TFKGNNNQNK YIERINELVA YRKKSLIIEF SDVLSFNENL AYEIINNTKI ILPILEGALY DHILQLDPT YQRDIEKVHV RIVGIPRVIE LRKIRSTDIG KLITIDGILV KVTPVKERIY KATYKHIHPD CMQEFEWPED E EMPEVLEM ...String: SLEIPSKQID YRDVFIEFLT TFKGNNNQNK YIERINELVA YRKKSLIIEF SDVLSFNENL AYEIINNTKI ILPILEGALY DHILQLDPT YQRDIEKVHV RIVGIPRVIE LRKIRSTDIG KLITIDGILV KVTPVKERIY KATYKHIHPD CMQEFEWPED E EMPEVLEM PTICPKCGKP GQFRLIPEKT KLIDWQKAVI QERPEEVPSG QLPRQLEIIL EDDLVDSARP GDRVKVTGIL DI KQDSPVK RGSRAVFDIY MKVSSIEVSG GSGGSSEEDE KKIKDLAKDP WIRDRIISSI APSIYGHWEL KEALALALFG GVP KVLEDT RIRGDIHILI IGDPGTAKSQ MLQFISRVAP RAVYTTGKGS TAAGLTAAVV REKGTGEYYL EAGALVLADG GIAV IDEID KMRDEDRVAI HEAMEQQTVS IAKAGIVAKL NARAAVIAAG NPKFGRYISE RPVSDNINLP PTILSRFDLI FILKD QPGE QDRELANYIL DVHSGKSTKN IIDIDTLRKY IAYARKYVTP KITSEAKNLI TDFFVEMRKK SSETPDSPIL ITPRQL EAL IRISEAYAKM ALKAEVTRED AERAINIMRL FLESVGVDME SGKIDID UniProtKB: Minichromosome maintenance protein MCM |
-Macromolecule #2: 16-mer oligo-dT
Macromolecule | Name: 16-mer oligo-dT / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 4.822127 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT) |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-...
Macromolecule | Name: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium type: ligand / ID: 5 / Number of copies: 5 / Formula: 08T |
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Molecular weight | Theoretical: 492.201 Da |
Chemical component information | ![]() ChemComp-08T: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 15 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 78.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: B / Chain - Source name: PDB / Chain - Initial model type: experimental model |
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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. |
Refinement | Space: REAL / Protocol: OTHER |
Output model | ![]() PDB-8eah: |