[English] 日本語
Yorodumi
- SASDD45: Type II toxin-antitoxin system HicB family antitoxin - HicB protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDD45
SampleType II toxin-antitoxin system HicB family antitoxin - HicB protein
  • Type II toxin-antitoxin system HicB family antitoxin (protein), HicB, Burkholderia pseudomallei
Function / homology: / HicB-like antitoxin of toxin-antitoxin system / HicB_like antitoxin of bacterial toxin-antitoxin system / TTHA1013/TTHA0281-like / HicB-like antitoxin of toxin-antitoxin system domain-containing protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
CitationJournal: J Biol Chem / Year: 2018
Title: The molecular basis of protein toxin HicA-dependent binding of the protein antitoxin HicB to DNA.
Authors: Ashley J Winter / Christopher Williams / Michail N Isupov / Hannah Crocker / Mariya Gromova / Philip Marsh / Oliver J Wilkinson / Mark S Dillingham / Nicholas J Harmer / Richard W Titball / Matthew P Crump /
Abstract: Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which ...Toxin-antitoxin (TA) systems are present in many bacteria and play important roles in bacterial growth, physiology, and pathogenicity. Those that are best studied are the type II TA systems, in which both toxins and antitoxins are proteins. The HicAB system is one of the prototypic TA systems, found in many bacterial species. Complex interactions between the protein toxin (HicA), the protein antitoxin (HicB), and the DNA upstream of the encoding genes regulate the activity of this system, but few structural details are available about how HicA destabilizes the HicB-DNA complex. Here, we determined the X-ray structures of HicB and the HicAB complex to 1.8 and 2.5 Å resolution, respectively, and characterized their DNA interactions. This revealed that HicB forms a tetramer and HicA and HicB form a heterooctameric complex that involves structural reorganization of the C-terminal (DNA-binding) region of HicB. Our observations indicated that HicA has a profound impact on binding of HicB to DNA sequences upstream of in a stoichiometric-dependent way. At low ratios of HicA:HicB, there was no effect on DNA binding, but at higher ratios, the affinity for DNA declined cooperatively, driving dissociation of the HicA:HicB:DNA complex. These results reveal the structural mechanisms by which HicA de-represses the HicB-DNA complex.
Contact author
  • Ash Winter (University of Bristol)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #1880
Type: atomic / Chi-square value: 1.97526858112
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Type II toxin-antitoxin system HicB family antitoxin - HicB protein
Specimen concentration: 5 mg/ml
BufferName: 25 mM Tris 150 mM NaCl / pH: 7.5
Entity #1010Name: HicB / Type: protein
Description: Type II toxin-antitoxin system HicB family antitoxin
Formula weight: 15.739 / Num. of mol.: 4 / Source: Burkholderia pseudomallei / References: UniProt: Q63NA5
Sequence:
MMEFPIAVHK DDGSVYGVTV PDIPGVHSWG ETIDDAIKNT REAIVGHVET LIELGEDVEF TCSTVEELVA KPEYAGAVWA LVSVDLSQLD SKPERINVSI PRFVLHKIDA YVASRHETRS GFLARAALEA LNEGKKHHHH HH

-
Experimental information

BeamInstrument name: Diamond Light Source B21 / City: Oxfordshire / 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: Type II toxin-antitoxin system HicB family antitoxin - HicB protein
Measurement date: Jul 28, 2016 / Storage temperature: 4 °C / Cell temperature: 25 °C / Exposure time: 3 sec. / Unit: 1/A /
MinMax
Q0.004 0.4075
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 931 /
MinMax
Q0.00593908 0.261569
P(R) point1 931
R0 104.8
Result
Type of curve: sec
Comments: Analysis of the data involved ScÅtter (www.bioisis.net/). The resultant curve was fit with the crystal structure of HicB, PDB Code: 6G1N.
ExperimentalPorod
MW62 kDa70 kDa
Volume-112 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I00.003825 5.0E-5 0.00380685 1.0E-5
Radius of gyration, Rg3.098 nm0.06 3.04 nm0.056

MinMax
D-10.5
Guinier point35 121

+
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