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- EMDB-62291: Cryo-EM structure of AbCapV S58A filament bound with 3'3'-cGAMP w... -

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Basic information

Entry
Database: EMDB / ID: EMD-62291
TitleCryo-EM structure of AbCapV S58A filament bound with 3'3'-cGAMP with extra phospholipid density
Map data
Sample
  • Complex: AbCapV S58A with 3'3'-cGAMP
    • Protein or peptide: CGAMP-activated phospholipase CapV
  • Ligand: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
KeywordsCBASS / phospholipase / 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: 3.04 Å
AuthorsKong JP / Li ZX / Wu WQ / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of AbCapV
Authors: Kong JP
History
DepositionNov 5, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62291.png

Downloads & links

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Map

FileDownload / File: emd_62291.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.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.06355504 - 0.16338308
Average (Standard dev.)0.0011533163 (±0.008292066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_62291_additional_1.map
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Half map: #2

Fileemd_62291_half_map_1.map
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Half map: #1

Fileemd_62291_half_map_2.map
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Sample components

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Entire : AbCapV S58A with 3'3'-cGAMP

EntireName: AbCapV S58A with 3'3'-cGAMP
Components
  • Complex: AbCapV S58A with 3'3'-cGAMP
    • Protein or peptide: CGAMP-activated phospholipase CapV
  • Ligand: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one

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Supramolecule #1: AbCapV S58A with 3'3'-cGAMP

SupramoleculeName: AbCapV S58A with 3'3'-cGAMP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 6 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 41.291309 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: METSENKSEI KILSLNGGGV RGLFTITLLA ELESIIEKRE KCENVKIGDY FDLITGTAIG GILALGLASG KSARELKEAF EINATKIFP LKRFKNKQWW NLLRRSIYES EPLYDAVKSM IGETIKFEDL NRRVMITSVN LSTGKPKFFK TPHNPMFTMD R EIRLIDAA ...String:
METSENKSEI KILSLNGGGV RGLFTITLLA ELESIIEKRE KCENVKIGDY FDLITGTAIG 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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Macromolecule #2: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-...

MacromoleculeName: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2- ...Name: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one
type: ligand / ID: 2 / Number of copies: 6 / Formula: 4BW
Molecular weightTheoretical: 674.411 Da
Chemical component information

ChemComp-4BW:
2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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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: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 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: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204417
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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