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Open data
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Basic information
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Title | Duplex-G-quadruplex-duplex (DGD) class_1 | |||||||||
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![]() | G-quadruplex / promoter / duplex / DNA | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.4 Å | |||||||||
![]() | Monsen RC / Chua EYD / Hopkins JB / Chaires JB / Trent JO | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM. Authors: Robert C Monsen / Eugene Y D Chua / Jesse B Hopkins / Jonathan B Chaires / John O Trent / ![]() Abstract: Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are ...Genomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5' G-tetrad interface with a persistently unstacked 3' duplex. The surrogate complement poly dT loop preferably stacks onto the 3' G-tetrad interface resulting in occlusion of both 5' and 3' tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.9 KB | Display | ![]() |
Images | ![]() | 25.2 KB | ||
Filedesc metadata | ![]() | 4.9 KB | ||
Others | ![]() ![]() | 31.8 MB 31.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 652 KB | Display | ![]() |
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Full document | ![]() | 651.6 KB | Display | |
Data in XML | ![]() | 14.6 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dutMC ![]() 27725 ![]() 27727 M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.0252 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27726_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27726_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : synthetic duplex-G-quadruplex-duplex construct mimicking a promoter G4
Entire | Name: synthetic duplex-G-quadruplex-duplex construct mimicking a promoter G4 |
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Components |
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-Supramolecule #1: synthetic duplex-G-quadruplex-duplex construct mimicking a promoter G4
Supramolecule | Name: synthetic duplex-G-quadruplex-duplex construct mimicking a promoter G4 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Duplex-G-quadruplex-duplex (46-MER)
Macromolecule | Name: Duplex-G-quadruplex-duplex (46-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.086031 KDa |
Sequence | String: (DG)(DC)(DG)(DT)(DG)(DC)(DC)(DG)(DC)(DA) (DT)(DT)(DA)(DA)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DG)(DT)(DA) (DT) (DA)(DC)(DA)(DT)(DA)(DG) |
-Macromolecule #2: Duplex-G-quadruplex-duplex (46-MER)
Macromolecule | Name: Duplex-G-quadruplex-duplex (46-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 14.407232 KDa |
Sequence | String: (DC)(DT)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DC) (DA)(DA)(DA)(DG)(DA)(DG)(DG)(DG)(DT)(DG) (DG)(DG)(DT)(DA)(DG)(DG)(DG)(DT)(DG) (DG)(DG)(DT)(DT)(DT)(DA)(DA)(DT)(DG)(DC) (DG) (DG)(DC)(DA)(DC)(DG)(DC) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | 2D array |
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Sample preparation
Concentration | 2.5 mg/mL | ||||||||||||
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Buffer | pH: 7.2 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV | ||||||||||||
Details | Sample was monodisperse. |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 12175 / Average exposure time: 0.4 sec. / Average electron dose: 68.54 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: 2.7 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: HELIUM |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 557.2 / Target criteria: map correlation |
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Output model | ![]() PDB-8dut: |