[English] 日本語
Yorodumi
- SASDEJ6: Complex of Epstein-Barr nuclear antigen 2 (EBNA2 Type1, amino aci... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDEJ6
SampleComplex of Epstein-Barr nuclear antigen 2 (EBNA2 Type1, amino acids 381-455) and BS69 (Zinc finger MYND domain-containing protein 11: CC-MYND, amino acids 480-602)
  • Epstein-Barr nuclear antigen 2 (protein), EBNA2 Type1, Epstein-Barr virus (strain B95-8)
  • Zinc finger MYND domain-containing protein 11 (protein), BS69 CC-MYND, Homo sapiens
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle progression / host cell nuclear matrix / protein serine/threonine phosphatase inhibitor activity / symbiont-mediated perturbation of host transcription / DNA-templated viral transcription / symbiont-mediated suppression of host translation initiation / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / host cell nucleus / positive regulation of DNA-templated transcription
Similarity search - Function
Epstein-Barr nuclear antigen 2 / Isoform 1 of Zinc finger MYND domain-containing protein 11
Similarity search - Component
Biological speciesEpstein-Barr virus (strain B95-8) (Epstein-Barr virus (strain B95-8))
Homo sapiens (human)
CitationDate: 2018 Nov 6
Title: Increased association between Epstein-Barr virus EBNA2 from type 2 strains and the transcriptional repressor BS69 restricts B cell growth
Authors: Ponnusamy R / Khatri R / Correia P / Mancini E / Farrell P
Contact author
  • Rajesh Ponnusamy (University of Sussex, Brighton, UK)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2541
Type: dummy / Radius of dummy atoms: 3.00 A / Chi-square value: 1.400 / P-value: 0.000312
Search similar-shape structures of this assembly by Omokage search (details)
Model #2549
Type: dummy / Radius of dummy atoms: 3.00 A / Chi-square value: 1.400 / P-value: 0.000312
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Complex of Epstein-Barr nuclear antigen 2 (EBNA2 Type1, amino acids 381-455) and BS69 (Zinc finger MYND domain-containing protein 11: CC-MYND, amino acids 480-602)
Specimen concentration: 9 mg/ml / Entity id: 1341 / 1343
BufferName: 20mM Tris-HCl, 100mM NaCl, 2% Sucrose and 1mM TCEP / pH: 7.5
Entity #1341Name: EBNA2 Type1 / Type: protein / Description: Epstein-Barr nuclear antigen 2 / Formula weight: 7.831 / Num. of mol.: 2 / Source: Epstein-Barr virus (strain B95-8) / References: UniProt: P12978
Sequence:
SMPELSPVLG LHQGQGAGDS PTPGPSNAAP VCRNSHTATP NVSPIHEPES HNSPEAPILF PDDWYPPSID PADLD
Entity #1343Name: BS69 CC-MYND / Type: protein / Description: Zinc finger MYND domain-containing protein 11 / Formula weight: 15.064 / Num. of mol.: 4 / Source: Homo sapiens / References: UniProt: Q15326-1
Sequence:
DRMKSDHKRE TERVVREALE KLRSEMEEEK RQAVNKAVAN MQGEMDRKCK QVKEKCKEEF VEEIKKLATQ HKQLISQTKK KQWCYNCEEE AMYHCCWNTS YCSIKCQQEH WHAEHKRTCR RKR

-
Experimental information

BeamInstrument name: Diamond Light Source B21 / City: Didcot / 国: UK / Shape: 1 x 5 mm / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 4.014 mm
DetectorName: Pilatus 2M
Scan
Title: Complex of Epstein-Barr nuclear antigen 2 (EBNA2 Type1, amino acids 381-455) and BS69 (Zinc finger MYND domain-containing protein 11: CC-MYND, amino acids 480-602)
Measurement date: Nov 29, 2017 / Storage temperature: 4 °C / Cell temperature: 25 °C / Exposure time: 3 sec. / Number of frames: 25 / Unit: 1/A /
MinMax
Q0.0103 0.2417
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 674 /
MinMax
Q0.0102666 0.159107
P(R) point1 674
R0 138.3
Result
Type of curve: sec
Comments: SEC-SAXS was performed using the following parameters: Column type: S200 3.2/300 increase; Flow rate: 0.075 ml/min; Injection volume: 45 µl; Sample injection concentration: 9.0 mg/ml. The ...Comments: SEC-SAXS was performed using the following parameters: Column type: S200 3.2/300 increase; Flow rate: 0.075 ml/min; Injection volume: 45 µl; Sample injection concentration: 9.0 mg/ml. The molar ratio of the injected sample components was 1:3 (EBNA2:BS69). The final complex contains four BS69 CC-MYND (2 dimers) with two EBNA2 Type1 (381-455) polypeptides.
ExperimentalPorod
MW69.4 kDa-
Volume-72 nm3

P(R)GuinierGuinier error
Forward scattering, I00.01062 0.0107 0.0001
Radius of gyration, Rg4.65 nm4.57 nm0.08

MinMax
D-13.83
Guinier point29 84

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more