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- EMDB-19579: ComM helicase hexamer in abscence o DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-19579
TitleComM helicase hexamer in abscence o DNA
Map data
Sample
  • Complex: ComM
    • Protein or peptide: Competence related protein ComM
  • 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.93 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 7, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19579.png

Downloads & links

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Map

FileDownload / File: emd_19579.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 330.24 Å		0.65 Å/pix.
x 512 pix.
= 330.24 Å		0.65 Å/pix.
x 512 pix.
= 330.24 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.003414578 - 0.0066376487
Average (Standard dev.)0.000005781654 (±0.00020595887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19579_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_19579_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_19579_half_map_2.map
Projections & Slices
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Sample components

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Entire : ComM

EntireName: ComM
Components
  • Complex: ComM
    • Protein or peptide: Competence related protein ComM
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

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Supramolecule #1: ComM

SupramoleculeName: ComM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Legionella pneumophila (bacteria)

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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

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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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

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78222
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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