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- EMDB-57548: Cryo-EM structure of Beta-lactamase-like domain from Neomoorella ... -

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Basic information

Entry
Database: EMDB / ID: EMD-57548
TitleCryo-EM structure of Beta-lactamase-like domain from Neomoorella carbonis
Map dataB-lactamase-like domain
Sample
  • Complex: Beta-lactamase-like domain
    • Protein or peptide: Beta-lactamase-like domain
KeywordsDNA translocation / Nuclease / DNA binding / MEMBRANE PROTEIN
Biological speciesNeomoorella carbonis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsDeselaers S / Wang D / Cairoli T / Afanasyev P / Hospenthal MK
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss State Secretariat for Education, Research and InnovationMB22.00043 Switzerland
Swiss National Science Foundation3200-0-239918 Switzerland
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structure and biochemistry reveal substrate-modulated ComEC nuclease activity during DNA processing.
Authors: Sophie Deselaers / Dianhong Wang / Tamino Cairoli / Pavel Afanasyev / Manuela K Hospenthal /
Abstract: Natural transformation enables bacteria to internalize extracellular DNA, driving adaptation and the spread of antibiotic resistance. The membrane protein ComEC mediates translocation of single- ...Natural transformation enables bacteria to internalize extracellular DNA, driving adaptation and the spread of antibiotic resistance. The membrane protein ComEC mediates translocation of single-stranded DNA (ssDNA) across the cytoplasmic membrane while degrading the complementary strand, yet the structural basis of its activity remains incompletely defined. Here, we report a cryo-electron microscopy structure of full-length ComEC from Neomoorella carbonis in a pre-translocation state, revealing a three-domain architecture and a conserved transmembrane channel captured in a closed conformation. Structural analysis indicates that conformational rearrangements of channel-lining helices would be required to accommodate ssDNA. Biochemical assays show that, relative to the isolated β-lactamase-like domain, full-length ComEC degrades DNA more efficiently and exhibits position-dependent cleavage of phosphodiester bonds within the DNA substrate. Importantly, coating of the DNA by the periplasmic DNA receptor ComEA suppresses endonucleolytic cleavage and enhances 5'' terminal cleavage, thereby directing ComEC towards productive processing of transforming DNA during natural transformation.
History
DepositionApr 20, 2026-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57548.png

Downloads & links

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Map

FileDownload / File: emd_57548.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-lactamase-like domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 256 pix.
= 259.072 Å		1.01 Å/pix.
x 256 pix.
= 259.072 Å		1.01 Å/pix.
x 256 pix.
= 259.072 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.012 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.157
Minimum - Maximum-0.9793604 - 1.1661866
Average (Standard dev.)0.00026823688 (±0.013178357)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 259.072 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: B-lactamase-like domain half map B

Fileemd_57548_half_map_1.map
AnnotationB-lactamase-like domain half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: B-lactamase-like domain half map A

Fileemd_57548_half_map_2.map
AnnotationB-lactamase-like domain half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Beta-lactamase-like domain

EntireName: Beta-lactamase-like domain
Components
  • Complex: Beta-lactamase-like domain
    • Protein or peptide: Beta-lactamase-like domain

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Supramolecule #1: Beta-lactamase-like domain

SupramoleculeName: Beta-lactamase-like domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: ComEC solublized in LMNG
Source (natural)Organism: Neomoorella carbonis (bacteria)
Molecular weightTheoretical: 87 KDa

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Macromolecule #1: Beta-lactamase-like domain

MacromoleculeName: Beta-lactamase-like domain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Neomoorella carbonis (bacteria)
Molecular weightTheoretical: 87.664914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIAAPLVRVT LAYICGLLLA SRITVGPVQL LALTVILWTL AYLFRQPPRR AAWQAFLLAG FMALGLLIST WDSSHHQSRL TGDRGTFLD LSGTVIEEPR VYANRVVYTL ATREIRQGDY HKRVKEKVQV VLYRPAEGGE PELYRYGDVL RVHGQLAAPP A ARNPGELD ...String:
MIAAPLVRVT LAYICGLLLA SRITVGPVQL LALTVILWTL AYLFRQPPRR AAWQAFLLAG FMALGLLIST WDSSHHQSRL TGDRGTFLD LSGTVIEEPR VYANRVVYTL ATREIRQGDY HKRVKEKVQV VLYRPAEGGE PELYRYGDVL RVHGQLAAPP A ARNPGELD YRAYLARQYI YNRMLINDPR AIVKLGTVPG HPLVRLALGA KARVKTVITA ALPPRQAGIL AALLFGDVNE LT DTDSDTF KNLGVFHFFA VSGSNTALVL LILMAIAGFL GLERSGAVFL GLAGLIFYAA VTGFTPSVSR AGIMAGLGLI AYL RREQRD FYTALALAAL VILLFRPRSL YDSGFQLSFA AAWGIVYFYP LLDDLLAWLP AWRACLVVPL AAQAATLPLV AYYF NFVSL LSLPANLVTA GLVGAIVTLG LAASTLALIT PAPAVMIFTA LGPLVNLLLA FLERLAGLPG ITIPLATPSP LAVAG YYLA LILWREFWLR RHEPRWQALW RWHRRELGLL AILTLATLLI FLYPPGRQEE LKVTFIDVGQ GDAVYLATPA GRHILV DGG GRPYGQGDFD VGERVVVPFL HRQGVRRLDV VISTHPDADH IGGLMAVVRE MPVSLVVVPP LRGGMLDAYR PFLAELQ AR GIPWQQAGRG DALALDPALN IQVLHPGREI SGSNSDSNNN SLVLKVIYRQ FSLFLSADIE TAAMADLMAS GADVRSTV F KVPHHGSRYG LEREFLKQVA PQVVVIPVGE KNNFGHPAPE ILSYWQEQGV PVYRTDRQGA ITIKSDGAHW QVDTTIPGG Y

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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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMHEPES-NaOH4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
50.0 mMNaClSodium Chloride
2.0 mMBeta-mercaptoethanolBeta-mercaptoethanol

Details: 0.01% (w/v) LMNG was added during affinity purification but excluded during SEC.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Pressure: 0.39 kPa
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3276527
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 383072
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.7.1) / Details: stochastic gradient descent (SGD) in CryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.7.1) / Details: Expectation Maximization
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-30bt:
Cryo-EM structure of Beta-lactamase-like domain from Neomoorella carbonis

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