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- EMDB-61417: Cryo-EM structure of AbCapV dimer, apo form -

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Basic information

Entry
Database: EMDB / ID: EMD-61417
TitleCryo-EM structure of AbCapV dimer, apo form
Map data
Sample
  • Complex: AbCapV dimer, apo form
    • Protein or peptide: CGAMP-activated phospholipase CapV
KeywordsCBASS / HYDROLASE
Function / homologyPatatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase / lipid catabolic process / hydrolase activity / CGAMP-activated phospholipase CapV
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKong JP / Li ZX / Ke SY / Wu WQ / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanisms of CBASS phospholipase effector CapV mediated membrane disruption.
Authors: Jianping Kong / Wanqian Wu / Shiyue Ke / Zihan Zhou / Shenglan Xia / Jianyu Chen / Runyu Zhu / Yijia Hou / Tinashe Makanyire / Xiangru Shan / Zhuyue Zhuo / Keying Li / Hongtao Shen / Pan ...Authors: Jianping Kong / Wanqian Wu / Shiyue Ke / Zihan Zhou / Shenglan Xia / Jianyu Chen / Runyu Zhu / Yijia Hou / Tinashe Makanyire / Xiangru Shan / Zhuyue Zhuo / Keying Li / Hongtao Shen / Pan Yang / Pingping Huang / Jingxian Liu / Jing Li / Xiaolian Sun / Jiajia Dong / Hongbin Sun / Meirong Chen / Meiling Lu / Zhaoxing Li / Yibei Xiao /
Abstract: Cyclic oligonucleotide-based antiphage signaling systems (CBASS) are widespread bacterial immune systems that trigger host suicide via cyclic nucleotide-activated effectors. The predominant strategy ...Cyclic oligonucleotide-based antiphage signaling systems (CBASS) are widespread bacterial immune systems that trigger host suicide via cyclic nucleotide-activated effectors. The predominant strategy to induce cell death in CBASS is membrane disruption. Here, we demonstrate that patatin-like phospholipase CapV, the most abundant CBASS effector, relocates and cleaves membrane phospholipids at the cell pole upon 3'3'-cGAMP binding, inducing polarized membrane disruption and cell death. Using cryo-EM, we reveal that apo-CapV adopts both dimeric and tetrameric states, with its phospholipid-binding pocket occluded and locked in an inactive conformation. Binding to 3'3'-cGAMP induces filamentation and substantial conformational change of CapV, enhancing membrane binding via electrostatic interactions between its interspaced basic surfaces and the negatively charged phosphate moieties of phospholipids. Simultaneously, the rearrangement opens the phospholipid-binding pocket, enabling the accommodation of two fatty acid chains of phospholipid within distinct hydrophobic pockets. Our findings reveal a filament-dependent activation mechanism for phospholipase-mediated membrane disruption during antiviral response.
History
DepositionSep 3, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61417.png

Downloads & links

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Map

FileDownload / File: emd_61417.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å		0.73 Å/pix.
x 256 pix.
= 186.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.75738895 - 0.9907733
Average (Standard dev.)-0.000009044979 (±0.028498948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 186.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61417_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61417_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : AbCapV dimer, apo form

EntireName: AbCapV dimer, apo form
Components
  • Complex: AbCapV dimer, apo form
    • Protein or peptide: CGAMP-activated phospholipase CapV

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Supramolecule #1: AbCapV dimer, apo form

SupramoleculeName: AbCapV dimer, apo form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Acinetobacter baumannii (bacteria)

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Macromolecule #1: CGAMP-activated phospholipase CapV

MacromoleculeName: CGAMP-activated phospholipase CapV / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 41.307312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: METSENKSEI KILSLNGGGV RGLFTITLLA ELESIIEKRE KCENVKIGDY FDLITGTSIG GILALGLASG KSARELKEAF EINATKIFP LKRFKNKQWW NLLRRSIYES EPLYDAVKSM IGETIKFEDL NRRVMITSVN LSTGKPKFFK TPHNPMFTMD R EIRLIDAA ...String:
METSENKSEI KILSLNGGGV RGLFTITLLA ELESIIEKRE KCENVKIGDY FDLITGTSIG GILALGLASG KSARELKEAF EINATKIFP LKRFKNKQWW NLLRRSIYES EPLYDAVKSM IGETIKFEDL NRRVMITSVN LSTGKPKFFK TPHNPMFTMD R EIRLIDAA MATSAAPTYF KPHYIEKLEN YFADGGLVAN NPSYIGIREV LIDMKNDFPD AKPENIKVLN IGTLSEDYCI SP ETLSKNS GKGYLSLWNM GERIVLSTMT ANQHLQRFML LREFEALKIE KNYVEIDETI PNEAAAEITL DNASEGCLKA LRG SGKKLA AERYTKNEEL RNFFLKKAEP FVPYIESSEV TAHHHHHH

UniProtKB: CGAMP-activated phospholipase CapV

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 271245
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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