[English] 日本語
Yorodumi- EMDB-26305: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26305 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | EBV latency protein EBNA1 Dyad symmetry / VIRAL PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information host cell PML body / viral latency / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / enzyme-substrate adaptor activity / symbiont-mediated disruption of host cell PML body / regulation of DNA replication / symbiont-mediated suppression of host NF-kappaB cascade / endonuclease activity / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Mei Y / Lieberman P | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: To Be Published Title: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element Authors: Mei Y / Lieberman P | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_26305.map.gz | 80.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-26305-v30.xml emd-26305.xml | 17.2 KB 17.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26305_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_26305.png | 28.5 KB | ||
Filedesc metadata | emd-26305.cif.gz | 6.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26305 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26305 | HTTPS FTP |
-Validation report
Summary document | emd_26305_validation.pdf.gz | 480.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_26305_full_validation.pdf.gz | 479.7 KB | Display | |
Data in XML | emd_26305_validation.xml.gz | 11.7 KB | Display | |
Data in CIF | emd_26305_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26305 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26305 | HTTPS FTP |
-Related structure data
Related structure data | 7u1tMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_26305.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : EBNA1 DNA binding domain binds to half Dyad Symmetry region
Entire | Name: EBNA1 DNA binding domain binds to half Dyad Symmetry region |
---|---|
Components |
|
-Supramolecule #1: EBNA1 DNA binding domain binds to half Dyad Symmetry region
Supramolecule | Name: EBNA1 DNA binding domain binds to half Dyad Symmetry region type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
---|---|
Source (natural) | Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
Molecular weight | Theoretical: 160 KDa |
-Macromolecule #1: Epstein-Barr nuclear antigen 1
Macromolecule | Name: Epstein-Barr nuclear antigen 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) Strain: B95-8 |
Molecular weight | Theoretical: 19.243031 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: PADDPGEGPS TGPRGQGDGG RRKKGGWFGK HRGQGGSNPK FENIAEGLRA LLARSHVERT TDEGTWVAGV FVYGGSKTSL YNLRRGTAL AIPQCRLTPL SRLPFGMAPG PGPQPGPLRE SIVCYFMVFL QTHIFAEVLK DAIKDLVMTK PAPTCNIRVT V CSFDDGVD LPPWFPPMVE UniProtKB: Epstein-Barr nuclear antigen 1 |
-Macromolecule #2: DNA (59-MER)
Macromolecule | Name: DNA (59-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
Molecular weight | Theoretical: 18.181674 KDa |
Sequence | String: (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT) (DT)(DC)(DG)(DA)(DT)(DA)(DG)(DC)(DA)(DT) (DA)(DT)(DG)(DC)(DT)(DT)(DC)(DC)(DC) (DG)(DT)(DT)(DG)(DG)(DG)(DT)(DA)(DA)(DC) (DA) (DT)(DA)(DT)(DG)(DC)(DT) ...String: (DT)(DA)(DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT) (DT)(DC)(DG)(DA)(DT)(DA)(DG)(DC)(DA)(DT) (DA)(DT)(DG)(DC)(DT)(DT)(DC)(DC)(DC) (DG)(DT)(DT)(DG)(DG)(DG)(DT)(DA)(DA)(DC) (DA) (DT)(DA)(DT)(DG)(DC)(DT)(DA)(DT) (DT)(DG)(DA)(DA)(DT)(DT)(DA)(DG)(DG)(DG) (DT) GENBANK: GENBANK: M80517.1 |
-Macromolecule #3: DNA (59-MER)
Macromolecule | Name: DNA (59-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: Human herpesvirus 4 strain B95-8 (Epstein-Barr virus (strain B95-8)) |
Molecular weight | Theoretical: 18.177703 KDa |
Sequence | String: (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DT) (DG)(DT)(DT)(DA)(DC)(DC)(DC)(DA)(DA) (DC)(DG)(DG)(DG)(DA)(DA)(DG)(DC)(DA)(DT) (DA) (DT)(DG)(DC)(DT)(DA)(DT) ...String: (DA)(DC)(DC)(DC)(DT)(DA)(DA)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DG)(DC)(DA)(DT)(DA)(DT) (DG)(DT)(DT)(DA)(DC)(DC)(DC)(DA)(DA) (DC)(DG)(DG)(DG)(DA)(DA)(DG)(DC)(DA)(DT) (DA) (DT)(DG)(DC)(DT)(DA)(DT)(DC)(DG) (DA)(DA)(DT)(DT)(DA)(DG)(DG)(DG)(DT)(DT) (DA) GENBANK: GENBANK: M80517.1 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.9 Component:
| ||||||||||||
Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 30.0 kPa | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 21 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4938 / Average exposure time: 1.68 sec. / Average electron dose: 1.03 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 30.0 µm / Calibrated defocus min: 10.0 µm / Calibrated magnification: 105000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 30.0 µm / Nominal defocus min: 10.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model |
| ||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 135 | ||||||||||||||
Output model | PDB-7u1t: |