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- EMDB-32258: Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) -
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Open data
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Basic information
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Title | Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) | |||||||||
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![]() | replication / CELL CYCLE-DNA complex | |||||||||
Function / homology | ![]() Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / single-stranded 3'-5' DNA helicase activity / regulation of phosphorylation / MCM complex / mitotic DNA replication initiation ...Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / single-stranded 3'-5' DNA helicase activity / regulation of phosphorylation / MCM complex / mitotic DNA replication initiation / double-strand break repair via break-induced replication / regulation of DNA-templated DNA replication initiation / single-stranded DNA helicase activity / DNA strand elongation involved in DNA replication / cochlea development / DNA unwinding involved in DNA replication / 3'-5' DNA helicase activity / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / cellular response to interleukin-4 / Activation of ATR in response to replication stress / Assembly of the pre-replicative complex / Orc1 removal from chromatin / nucleosome assembly / cellular response to xenobiotic stimulus / single-stranded DNA binding / histone binding / DNA helicase / DNA replication / cell population proliferation / cell cycle / chromosome, telomeric region / centrosome / apoptotic process / DNA damage response / chromatin / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.59 Å | |||||||||
![]() | Li J / Dong J / Dang S / Zhai Y | |||||||||
Funding support | ![]()
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![]() | ![]() Title: The human pre-replication complex is an open complex. Authors: Jian Li / Jiangqing Dong / Weitao Wang / Daqi Yu / Xinyu Fan / Yan Chit Hui / Clare S K Lee / Wai Hei Lam / Nathan Alary / Yang Yang / Yingyi Zhang / Qian Zhao / Chun-Long Chen / Bik-Kwoon ...Authors: Jian Li / Jiangqing Dong / Weitao Wang / Daqi Yu / Xinyu Fan / Yan Chit Hui / Clare S K Lee / Wai Hei Lam / Nathan Alary / Yang Yang / Yingyi Zhang / Qian Zhao / Chun-Long Chen / Bik-Kwoon Tye / Shangyu Dang / Yuanliang Zhai / ![]() ![]() ![]() Abstract: In eukaryotes, DNA replication initiation requires assembly and activation of the minichromosome maintenance (MCM) 2-7 double hexamer (DH) to melt origin DNA strands. However, the mechanism for this ...In eukaryotes, DNA replication initiation requires assembly and activation of the minichromosome maintenance (MCM) 2-7 double hexamer (DH) to melt origin DNA strands. However, the mechanism for this initial melting is unknown. Here, we report a 2.59-Å cryo-electron microscopy structure of the human MCM-DH (hMCM-DH), also known as the pre-replication complex. In this structure, the hMCM-DH with a constricted central channel untwists and stretches the DNA strands such that almost a half turn of the bound duplex DNA is distorted with 1 base pair completely separated, generating an initial open structure (IOS) at the hexamer junction. Disturbing the IOS inhibits DH formation and replication initiation. Mapping of hMCM-DH footprints indicates that IOSs are distributed across the genome in large clusters aligning well with initiation zones designed for stochastic origin firing. This work unravels an intrinsic mechanism that couples DH formation with initial DNA melting to license replication initiation in human cells. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 229.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 31.6 KB 31.6 KB | Display Display | ![]() |
Images | ![]() | 78.6 KB | ||
Filedesc metadata | ![]() | 10.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 610.6 KB | Display | ![]() |
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Full document | ![]() | 610.2 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w1yMC M: atomic model generated by this map C: citing same article ( |
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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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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : human Mini-chromosome maintenance complex
+Supramolecule #1: human Mini-chromosome maintenance complex
+Supramolecule #2: DNA replication licensing factor MCM 2/3/4/5/6/7
+Supramolecule #3: DNA
+Macromolecule #1: DNA replication licensing factor MCM2
+Macromolecule #2: Isoform 2 of DNA replication licensing factor MCM3
+Macromolecule #3: DNA replication licensing factor MCM4
+Macromolecule #4: DNA replication licensing factor MCM5
+Macromolecule #5: DNA replication licensing factor MCM6
+Macromolecule #6: DNA replication licensing factor MCM7
+Macromolecule #7: DNA (49-MER)
+Macromolecule #8: DNA (49-MER)
+Macromolecule #9: ZINC ION
+Macromolecule #10: MAGNESIUM ION
+Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE
-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: 7.5 Component:
Details: Solutions were made fresh from concentrated to avoid microbial contamination | |||||||||||||||||||||||||||||||||
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | |||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||||||||||||||
Details | This sample was monodisperse |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3710 / Average electron dose: 51.78 e/Å2 Details: Movies are collected in movie-mode containing 40 frames. |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |