[English] 日本語
![](img/lk-miru.gif)
- EMDB-26305: EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | EBNA1 DNA binding domain (401-641) binds to half Dyad Symmetry element | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | EBV latency protein EBNA1 Dyad symmetry / VIRAL PROTEIN-DNA complex | |||||||||
Function / homology | ![]() host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / 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 / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response ...host cell PML body / symbiont-mediated suppression of host antigen processing and presentation / 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 / endonuclease activity / DNA-binding transcription factor activity / virus-mediated perturbation of host defense response / positive regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Mei Y / Lieberman P | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 | ![]() | 80.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.2 KB 17.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 28.5 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 480.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 479.7 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u1tMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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: ![]() |
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: ![]() Strain: B95-8 |
Molecular weight | Theoretical: 19.243031 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() |
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: ![]() |
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 |
---|---|
![]() | 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: ![]() |
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: |