[English] 日本語
Yorodumi
- EMDB-12051: S. agalactiae BusR in complex with its busAB-promotor DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12051
TitleS. agalactiae BusR in complex with its busAB-promotor DNA
Map data
Sample
  • Complex: transcriptional repressor BusR bound to DNA
    • Complex: GntR family transcriptional regulator
      • Protein or peptide: GntR family transcriptional regulator
    • Complex: BusR binding site in the busAB promotor DNA
      • DNA: BusR binding site in the busAB promotor. strand1
      • DNA: BusR binding site in the busAB promotor. strand2
  • Ligand: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide
KeywordsRepressor / complex / GntR / DNA BINDING PROTEIN
Function / homology
Function and homology information


monoatomic cation transmembrane transporter activity / potassium ion transport / DNA-binding transcription factor activity
Similarity search - Function
: / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
GntR family transcriptional regulator
Similarity search - Component
Biological speciesStreptococcus agalactiae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.1 Å
AuthorsBandera AM / Witte G
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI3717/3-1 Germany
German Research Foundation (DFG)GRK1721 Germany
CitationJournal: Nucleic Acids Res / Year: 2021
Title: BusR senses bipartite DNA binding motifs by a unique molecular ruler architecture.
Authors: Adrian M Bandera / Joseph Bartho / Katja Lammens / David Jan Drexler / Jasmin Kleinschwärzer / Karl-Peter Hopfner / Gregor Witte /
Abstract: The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with ...The cyclic dinucleotide second messenger c-di-AMP is a major player in regulation of potassium homeostasis and osmolyte transport in a variety of bacteria. Along with various direct interactions with proteins such as potassium channels, the second messenger also specifically binds to transcription factors, thereby altering the processes in the cell on the transcriptional level. We here describe the structural and biochemical characterization of BusR from the human pathogen Streptococcus agalactiae. BusR is a member of a yet structurally uncharacterized subfamily of the GntR family of transcription factors that downregulates transcription of the genes for the BusA (OpuA) glycine-betaine transporter upon c-di-AMP binding. We report crystal structures of full-length BusR, its apo and c-di-AMP bound effector domain, as well as cryo-EM structures of BusR bound to its operator DNA. Our structural data, supported by biochemical and biophysical data, reveal that BusR utilizes a unique domain assembly with a tetrameric coiled-coil in between the binding platforms, serving as a molecular ruler to specifically recognize a 22 bp separated bipartite binding motif. Binding of c-di-AMP to BusR induces a shift in equilibrium from an inactivated towards an activated state that allows BusR to bind the target DNA, leading to transcriptional repression.
History
DepositionDec 7, 2020-
Header (metadata) releaseAug 11, 2021-
Map releaseAug 11, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7b5y
  • Surface level: 0.0232
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12051.png

Downloads & links

-
Map

FileDownload / File: emd_12051.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 220 pix.
= 232.98 Å		1.06 Å/pix.
x 220 pix.
= 232.98 Å		1.06 Å/pix.
x 220 pix.
= 232.98 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.059 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0232 / Movie #1: 0.0232
Minimum - Maximum-0.04612871 - 0.09732697
Average (Standard dev.)0.0003495504 (±0.0034157087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 232.98001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z232.980232.980232.980
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0460.0970.000

-
Supplemental data

-
Mask #1

Fileemd_12051_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_12051_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_12051_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : transcriptional repressor BusR bound to DNA

EntireName: transcriptional repressor BusR bound to DNA
Components
  • Complex: transcriptional repressor BusR bound to DNA
    • Complex: GntR family transcriptional regulator
      • Protein or peptide: GntR family transcriptional regulator
    • Complex: BusR binding site in the busAB promotor DNA
      • DNA: BusR binding site in the busAB promotor. strand1
      • DNA: BusR binding site in the busAB promotor. strand2
  • Ligand: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide

-
Supramolecule #1: transcriptional repressor BusR bound to DNA

SupramoleculeName: transcriptional repressor BusR bound to DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 123 KDa

-
Supramolecule #2: GntR family transcriptional regulator

SupramoleculeName: GntR family transcriptional regulator / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Streptococcus agalactiae (bacteria)

-
Supramolecule #3: BusR binding site in the busAB promotor DNA

SupramoleculeName: BusR binding site in the busAB promotor DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Streptococcus agalactiae (bacteria)

-
Macromolecule #1: GntR family transcriptional regulator

MacromoleculeName: GntR family transcriptional regulator / type: protein_or_peptide / ID: 1
Details: N-terminal residues GP result from purification tag
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus agalactiae (bacteria)
Molecular weightTheoretical: 23.88016 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPMVSEQSEI VTSKYQKIAV AVAQRIANGD YEVGEKLKSR TTIASTFNVS PETARKGLNI LADLQILTLK HGSGAIILSK EKAIEFLNQ YETSHSVAIL KGKIRDNIKA QQQEMEELAT LVDDFLLQTR AVSKQYPLAP YEIIVSEDSE HLGKSIGELN V WHQTGATI ...String:
GPMVSEQSEI VTSKYQKIAV AVAQRIANGD YEVGEKLKSR TTIASTFNVS PETARKGLNI LADLQILTLK HGSGAIILSK EKAIEFLNQ YETSHSVAIL KGKIRDNIKA QQQEMEELAT LVDDFLLQTR AVSKQYPLAP YEIIVSEDSE HLGKSIGELN V WHQTGATI VAIEHEGKFI VSPGPFSVIE QGDHIFFVGD EDVYARMKTY FNLRMGL

UniProtKB: GntR family transcriptional regulator

-
Macromolecule #2: BusR binding site in the busAB promotor. strand1

MacromoleculeName: BusR binding site in the busAB promotor. strand1 / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptococcus agalactiae (bacteria)
Molecular weightTheoretical: 14.309208 KDa
SequenceString:
(DC)(DG)(DG)(DT)(DA)(DA)(DA)(DG)(DT)(DG) (DA)(DC)(DG)(DT)(DT)(DA)(DA)(DA)(DG)(DT) (DA)(DT)(DC)(DG)(DT)(DA)(DA)(DA)(DA) (DG)(DG)(DG)(DT)(DA)(DG)(DT)(DC)(DA)(DC) (DT) (DT)(DT)(DT)(DC)(DG)(DG)

-
Macromolecule #3: BusR binding site in the busAB promotor. strand2

MacromoleculeName: BusR binding site in the busAB promotor. strand2 / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Streptococcus agalactiae (bacteria)
Molecular weightTheoretical: 14.020027 KDa
SequenceString:
(DC)(DC)(DG)(DA)(DA)(DA)(DA)(DG)(DT)(DG) (DA)(DC)(DT)(DA)(DC)(DC)(DC)(DT)(DT)(DT) (DT)(DA)(DC)(DG)(DA)(DT)(DA)(DC)(DT) (DT)(DT)(DA)(DA)(DC)(DG)(DT)(DC)(DA)(DC) (DT) (DT)(DT)(DA)(DC)(DC)(DG)

-
Macromolecule #4: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-...

MacromoleculeName: (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide
type: ligand / ID: 4 / Number of copies: 2 / Formula: 2BA
Molecular weightTheoretical: 658.412 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 6.5 / Component - Concentration: 20.0 mM / Component - Formula: HEPES / Component - Name: hepes / Details: degassed, filtered
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 7 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: LEICA EM GP
Details: 0.05% beta-octyl glycoside added prior to plunge freezing.
Detailshomogeneous and monodisperse sample

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 370421 / Details: CryoSparc blob-picker
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7b5t


Details: Structure of ligand-free full-length BusR
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20342
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

7b5t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7b5y:
S. agalactiae BusR in complex with its busAB-promotor DNA

+
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