[English] 日本語
Yorodumi
- EMDB-45181: The structure of two MntR dimers bound to the native mnep promote... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-45181
TitleThe structure of two MntR dimers bound to the native mnep promoter sequence.
Map dataSharpened cryo-EM map of 2 MntR dimers bound to the native mnep sequence.
Sample
  • Complex: MntR bound to mnep promoter sequence
    • Complex: MntR
      • Protein or peptide: HTH-type transcriptional regulator MntR
    • Complex: mnep promoter sequence
      • DNA: DNA (39-MER)
      • DNA: DNA (38-MER)
  • Ligand: MANGANESE (II) ION
KeywordsManganese / metal ion homeostasis / transcription regulation / transcription activation / cooperative binding / GENE REGULATION
Function / homology
Function and homology information


intracellular manganese ion homeostasis / manganese ion binding / protein dimerization activity / DNA-binding transcription factor activity / DNA binding / cytoplasm
Similarity search - Function
HTH-type transcription regulator MntR / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element ...HTH-type transcription regulator MntR / : / DtxR-type HTH domain profile. / DTXR-type HTH domain / Iron dependent repressor, N-terminal DNA binding domain / Iron dependent repressor, metal binding and dimerisation domain / Iron dependent repressor / Iron dependent repressor, metal binding and dimerisation domain superfamily / Iron dependent repressor, metal binding and dimerisation domain / Helix-turn-helix diphteria tox regulatory element / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
HTH-type transcriptional regulator MntR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 Å
AuthorsShi H / Fu Y / Glasfeld A / Ahuja S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The structure of two MntR dimers bound to the native mnep promoter sequence.
Authors: Shi H / Fu Y / Glasfeld A / Ahuja S
History
DepositionJun 4, 2024-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Downloads & links

-
Map

FileDownload / File: emd_45181.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM map of 2 MntR dimers bound to the native mnep sequence.
Voxel sizeX=Y=Z: 0.99844 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.2651898 - 1.9341338
Average (Standard dev.)0.00041640672 (±0.023269236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 255.60065 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : MntR bound to mnep promoter sequence

EntireName: MntR bound to mnep promoter sequence
Components
  • Complex: MntR bound to mnep promoter sequence
    • Complex: MntR
      • Protein or peptide: HTH-type transcriptional regulator MntR
    • Complex: mnep promoter sequence
      • DNA: DNA (39-MER)
      • DNA: DNA (38-MER)
  • Ligand: MANGANESE (II) ION

-
Supramolecule #1: MntR bound to mnep promoter sequence

SupramoleculeName: MntR bound to mnep promoter sequence / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

-
Supramolecule #2: MntR

SupramoleculeName: MntR / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bacillus subtilis (bacteria)

-
Supramolecule #3: mnep promoter sequence

SupramoleculeName: mnep promoter sequence / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Bacillus subtilis (bacteria) / Synthetically produced: Yes

-
Macromolecule #1: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.936714 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DG) (DT)(DC)(DA)(DC)(DC)(DT)(DT)(DA)(DT)(DT) (DT)(DA)(DT)(DT)(DA)(DG)(DT)(DA)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DA)(DA)(DC)(DA)

-
Macromolecule #2: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 11.748625 KDa
SequenceString:
(DT)(DG)(DT)(DT)(DT)(DC)(DC)(DT)(DG)(DT) (DT)(DT)(DA)(DC)(DT)(DA)(DA)(DT)(DA)(DA) (DA)(DT)(DA)(DA)(DG)(DG)(DT)(DG)(DA) (DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DA)

-
Macromolecule #3: HTH-type transcriptional regulator MntR

MacromoleculeName: HTH-type transcriptional regulator MntR / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 16.787133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTTPSMEDYI EQIYMLIEEK GYARVSDIAE ALAVHPSSVT KMVQKLDKDE YLIYEKYRGL VLTSKGKKIG KRLVYRHELL EQFLRIIGV DEEKIYNDVE GIEHHLSWNS IDRIGDLVQY FEEDDARKKD LKSIQKKTEH HNQ

UniProtKB: HTH-type transcriptional regulator MntR

-
Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MN
Molecular weightTheoretical: 54.938 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1on1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 194072
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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://pdbjlc1.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