[English] 日本語
Yorodumi
- EMDB-11022: Allostery through DNA drives phenotype switching -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11022
TitleAllostery through DNA drives phenotype switching
Map data
Sample
  • Complex: ComK transcription factor bound to its comG promoter DNA.
    • DNA: comG promoter DNA - strand A
    • DNA: comG promoter DNA - strand B
KeywordsTranscription-factor / DNA-binding / A-tract / Allostery / DNA BINDING PROTEIN
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsRosenblum G / Elad N
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation1549/15 Israel
CitationJournal: Nat Commun / Year: 2021
Title: Allostery through DNA drives phenotype switching.
Authors: Gabriel Rosenblum / Nadav Elad / Haim Rozenberg / Felix Wiggers / Jakub Jungwirth / Hagen Hofmann /
Abstract: Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that also DNA is capable of transmitting allosteric signals. Yet, whether and how DNA-mediated allostery ...Allostery is a pervasive principle to regulate protein function. Growing evidence suggests that also DNA is capable of transmitting allosteric signals. Yet, whether and how DNA-mediated allostery plays a regulatory role in gene expression remained unclear. Here, we show that DNA indeed transmits allosteric signals over long distances to boost the binding cooperativity of transcription factors. Phenotype switching in Bacillus subtilis requires an all-or-none promoter binding of multiple ComK proteins. We use single-molecule FRET to demonstrate that ComK-binding at one promoter site increases affinity at a distant site. Cryo-EM structures of the complex between ComK and its promoter demonstrate that this coupling is due to mechanical forces that alter DNA curvature. Modifications of the spacer between sites tune cooperativity and show how to control allostery, which allows a fine-tuning of the dynamic properties of genetic circuits.
History
DepositionMay 11, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6z0s
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6z0s
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11022.png

Downloads & links

-
Map

FileDownload / File: emd_11022.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 343.6 Å		0.86 Å/pix.
x 400 pix.
= 343.6 Å		0.86 Å/pix.
x 400 pix.
= 343.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.859 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.04815607 - 0.23668092
Average (Standard dev.)0.000028744202 (±0.0070220917)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 343.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8590.8590.859
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z343.600343.600343.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0480.2370.000

-
Supplemental data

-
Mask #1

Fileemd_11022_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_11022_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_11022_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ComK transcription factor bound to its comG promoter DNA.

EntireName: ComK transcription factor bound to its comG promoter DNA.
Components
  • Complex: ComK transcription factor bound to its comG promoter DNA.
    • DNA: comG promoter DNA - strand A
    • DNA: comG promoter DNA - strand B

-
Supramolecule #1: ComK transcription factor bound to its comG promoter DNA.

SupramoleculeName: ComK transcription factor bound to its comG promoter DNA.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (bacteria)

-
Macromolecule #1: comG promoter DNA - strand A

MacromoleculeName: comG promoter DNA - strand A / type: dna / ID: 1 / Details: 84-mer modeled upon 93 nucleotides / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 28.476242 KDa
SequenceString: (DC)(DA)(DG)(DT)(DT)(DG)(DA)(DA)(DA)(DG) (DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT) (DT)(DG)(DC)(DC)(DA)(DG)(DA)(DA)(DA) (DG)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DT)(DT) (DT) (DT)(DC)(DA)(DG)(DC)(DA) ...String:
(DC)(DA)(DG)(DT)(DT)(DG)(DA)(DA)(DA)(DG) (DT)(DC)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT) (DT)(DG)(DC)(DC)(DA)(DG)(DA)(DA)(DA) (DG)(DA)(DA)(DT)(DT)(DG)(DG)(DT)(DT)(DT) (DT) (DT)(DC)(DA)(DG)(DC)(DA)(DT)(DA) (DT)(DA)(DA)(DC)(DA)(DT)(DC)(DT)(DC)(DA) (DC)(DA) (DA)(DA)(DA)(DT)(DC)(DA)(DC) (DG)(DT)(DT)(DT)(DT)(DC)(DC)(DC)(DT)(DG) (DT)(DT)(DT) (DG)(DA)(DT)(DT)(DA)(DC) (DC)(DT)(DT)(DT)(DT)(DC)(DT)

-
Macromolecule #2: comG promoter DNA - strand B

MacromoleculeName: comG promoter DNA - strand B / type: dna / ID: 2 / Details: 86-mer modeled upon 93 nucleotides / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 28.882619 KDa
SequenceString: (DA)(DG)(DA)(DA)(DA)(DA)(DG)(DG)(DT)(DA) (DA)(DT)(DC)(DA)(DA)(DA)(DC)(DA)(DG)(DG) (DG)(DA)(DA)(DA)(DA)(DC)(DG)(DT)(DG) (DA)(DT)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DG) (DA) (DT)(DG)(DT)(DT)(DA)(DT) ...String:
(DA)(DG)(DA)(DA)(DA)(DA)(DG)(DG)(DT)(DA) (DA)(DT)(DC)(DA)(DA)(DA)(DC)(DA)(DG)(DG) (DG)(DA)(DA)(DA)(DA)(DC)(DG)(DT)(DG) (DA)(DT)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DG) (DA) (DT)(DG)(DT)(DT)(DA)(DT)(DA)(DT) (DG)(DC)(DT)(DG)(DA)(DA)(DA)(DA)(DA)(DC) (DC)(DA) (DA)(DT)(DT)(DC)(DT)(DT)(DT) (DC)(DT)(DG)(DG)(DC)(DA)(DA)(DG)(DA)(DA) (DA)(DA)(DA) (DA)(DG)(DA)(DC)(DT)(DT) (DT)(DC)(DA)(DA)(DC)(DT)(DG)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.24 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris
50.0 mMC6H14N4O2Arginine
150.0 mMKClKCl
5.0 mMMgCl2MgCl2
3.0 mMC4H10O2S2Dithiothreitol
0.001 %C58H114O26Tween-20
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse complex with dsDNA and 4 ComK equivalents.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average exposure time: 2.0 sec. / Average electron dose: 55.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 58207 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Details: Sequence adapted idealized B-DNA fiber like duplex produced using Coot.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 88140
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6z0s:
Allostery through DNA drives phenotype switching

+
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