[English] 日本語
Yorodumi
- EMDB-19574: ComM helicase from Legionella pneumophila, coordinating dsDNA and... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19574
TitleComM helicase from Legionella pneumophila, coordinating dsDNA and AMP-PNP
Map data
Sample
  • Complex: ComM hexameric helicase from Legionella pneumophila, coordinating dsDNA and AMPPNP
    • Protein or peptide: Competence related protein ComM
    • DNA: Poly-dT
    • DNA: Poly-dA Poly-dC
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
KeywordsHelicase Translocase natural transformation / DNA BINDING PROTEIN
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
Mg chelatase-related protein / Mg chelatase-related protein, C-terminal domain / Magnesium chelatase, subunit ChlI C-terminal / Subunit ChlI of Mg-chelatase / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities ...Mg chelatase-related protein / Mg chelatase-related protein, C-terminal domain / Magnesium chelatase, subunit ChlI C-terminal / Subunit ChlI of Mg-chelatase / Magnesium-chelatase subunit ChlI-like / Magnesium chelatase ChlI-like, catalytic domain / Magnesium chelatase, subunit ChlI / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Competence related protein ComM
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsTalachia Rosa L / Fronzes R
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: EMBO J / Year: 2024
Title: Structural insights into the mechanism of DNA branch migration during homologous recombination in bacteria.
Authors: Leonardo Talachia Rosa / Émeline Vernhes / Anne-Lise Soulet / Patrice Polard / Rémi Fronzes /
Abstract: Some DNA helicases play central and specific roles in genome maintenance and plasticity through their branch migration activity in different pathways of homologous recombination. RadA is a highly ...Some DNA helicases play central and specific roles in genome maintenance and plasticity through their branch migration activity in different pathways of homologous recombination. RadA is a highly conserved bacterial helicase involved in DNA repair throughout all bacterial species. In Gram-positive Firmicutes, it also has a role in natural transformation, while in Gram-negative bacteria, ComM is the canonical transformation-specific helicase. Both RadA and ComM helicases form hexameric rings and use ATP hydrolysis as an energy source to propel themselves along DNA. In this study, we present the cryoEM structures of RadA and ComM interacting with DNA and ATP analogs. These structures reveal important molecular interactions that couple ATP hydrolysis and DNA binding in RadA, as well as the role of the Lon protease-like domain, shared by RadA and ComM, in this process. Taken together, these results provide new molecular insights into the mechanisms of DNA branch migration in different pathways of homologous recombination.
History
DepositionFeb 6, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19574.png

Downloads & links

-
Map

FileDownload / File: emd_19574.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 500 pix.
= 322.5 Å		0.65 Å/pix.
x 500 pix.
= 322.5 Å		0.65 Å/pix.
x 500 pix.
= 322.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.36391097 - 0.86893535
Average (Standard dev.)0.0014747852 (±0.023457844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 322.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_19574_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_19574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_19574_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ComM hexameric helicase from Legionella pneumophila, coordinating...

EntireName: ComM hexameric helicase from Legionella pneumophila, coordinating dsDNA and AMPPNP
Components
  • Complex: ComM hexameric helicase from Legionella pneumophila, coordinating dsDNA and AMPPNP
    • Protein or peptide: Competence related protein ComM
    • DNA: Poly-dT
    • DNA: Poly-dA Poly-dC
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

-
Supramolecule #1: ComM hexameric helicase from Legionella pneumophila, coordinating...

SupramoleculeName: ComM hexameric helicase from Legionella pneumophila, coordinating dsDNA and AMPPNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Legionella pneumophila (bacteria)

-
Macromolecule #1: Competence related protein ComM

MacromoleculeName: Competence related protein ComM / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 55.849289 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLAFTKTRS TIGIVAQPVS VEVHLSNGLP SFTMVGLAET AVKESKDRVR SAIINSQFEF PCRKITVNLG PANLPKTGSG FDLPIALGI LAASEQIPLT NLANHEFIGE LALSGELRGV SAIIPAVLAA HKDNQHLIIA NANAAEASLT GHQKVFTANN L REVCDYLC ...String:
MSLAFTKTRS TIGIVAQPVS VEVHLSNGLP SFTMVGLAET AVKESKDRVR SAIINSQFEF PCRKITVNLG PANLPKTGSG FDLPIALGI LAASEQIPLT NLANHEFIGE LALSGELRGV SAIIPAVLAA HKDNQHLIIA NANAAEASLT GHQKVFTANN L REVCDYLC QGTSLQSLPP KPDLLLNNYE LDWSDIKGQQ HAKNAMVIAA CGGHSILLSG APGSGKTMMA KRFSTLLPEL SE TQALECA AINSIRGKLP DFREWRLPPF RAPHHTASPV ALVGGGNPPK PGEISLAHHG VLFLDELPEF NRQVLETLRE PLE SGHICI SRAAAQIEFP AKFQLIAAMN PCPCGQWGNS QANCMCTPDR ISRYLAKLSA PLLDRIDMQV TIHALSQEEL IKPN THLEK QSLAIREKVT KMHEIQMARQ DSLNANLNSK TCEMVCELGS EEQLFLREVM SKLKLSARGY HRLLKVSRTI ADMNS SKKV LLNHLQQALS YKQNLHLPKH HHHHH

UniProtKB: Competence related protein ComM

-
Macromolecule #2: Poly-dT

MacromoleculeName: Poly-dT / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.206602 KDa
SequenceString: (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT) ...String:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)

-
Macromolecule #3: Poly-dA Poly-dC

MacromoleculeName: Poly-dA Poly-dC / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 36.09834 KDa
SequenceString: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA) ...String:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA) (DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC)(DC) (DC)(DC)(DC)(DC)(DC)

-
Macromolecule #4: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 4 / Number of copies: 4 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.61 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 207233
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

+
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