[English] 日本語
Yorodumi
- EMDB-62334: Cryo-EM structure of lipase/ligand complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62334
TitleCryo-EM structure of lipase/ligand complex
Map data
Sample
  • Complex: complex of lipase and ligand
    • Protein or peptide: CBASS cGAMP-activated phospholipase
  • 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
Keywordslipase / HYDROLASE
Function / homology:
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLu DF / Zhu DY / Liu S
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Cell Rep / Year: 2026
Title: Structural mechanism of 3'3'-cGAMP-induced filamentation and phospholipid hydrolysis by CapV in bacterial antiphage defense.
Authors: Yun Lv / Sheng Liu / Qihai Wang / Jing Zhu / Yingxiang Hou / Haiyan Xu / Deyan Zhu / Yu Liu / Jing Wu / Changxin Wu / Guijun Shang / Hongxiang Lou / Defen Lu / Huiqing Yuan / Deyu Zhu /
Abstract: The cyclic-oligonucleotide-based antiphage signaling system (CBASS) protects bacteria from phage infection. In Vibrio cholerae, phage infection activates CD-NTase DncV to produce 3'3'-cGAMP, which ...The cyclic-oligonucleotide-based antiphage signaling system (CBASS) protects bacteria from phage infection. In Vibrio cholerae, phage infection activates CD-NTase DncV to produce 3'3'-cGAMP, which triggers phospholipase CapV to degrade phosphatidylethanolamine and phosphatidylglycerol, the major phospholipids in the inner-membranes, thereby inducing cell death. However, how 3'3'-cGAMP activates CapV was unclear. Here we present crystal structures of inactive Acinetobacter baumannii CapV in apo and 3'3'-cGAMP-bound forms, along with cryo-EM structures of activated CapV-3'3'-cGAMP complex, with or without substrate dioleoylphosphatidyl-ethanolamine (DOPE). Apo-CapV forms symmetric dimers in a "closed" state. 3'3'-cGAMP binding drives lateral polymerization of dimers into filament assembly, inducing an "open" state that exposes the active site and substrate-binding cleft. DOPE binding further shifts CapV to an "ajar" state, where a Y-shaped cleft positions DOPE for hydrolysis via a conserved Ser/Asp catalytic dyad. This 3'3'-cGAMP-induced filamentation mirrors activation mechanisms of TIR-STING, TIR-SAVED, and mammalian STING, revealing a conserved signaling pattern across immune systems.
History
DepositionNov 9, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_62334.png

Downloads & links

-
Map

FileDownload / File: emd_62334.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å		0.83 Å/pix.
x 256 pix.
= 212.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.5327373 - 2.3659291
Average (Standard dev.)0.004360059 (±0.08589738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 212.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_62334_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_62334_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : complex of lipase and ligand

EntireName: complex of lipase and ligand
Components
  • Complex: complex of lipase and ligand
    • Protein or peptide: CBASS cGAMP-activated phospholipase
  • 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

-
Supramolecule #1: complex of lipase and ligand

SupramoleculeName: complex of lipase and ligand / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Acinetobacter baumannii (bacteria)

-
Macromolecule #1: CBASS cGAMP-activated phospholipase

MacromoleculeName: CBASS cGAMP-activated phospholipase / type: protein_or_peptide / ID: 1
Details: Sequence reference for strain 'Acinetobacter baumannii' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A9E9MHI8.
Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Acinetobacter baumannii (bacteria)
Molecular weightTheoretical: 36.897059 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEKFQILALS GGGYRGLFTA TVLKELEQEA KENGHDSIAD CFDLITGTSV GGIVALAIAY GIKVEAIVDL FKSHGDKIFQ PKPFLKFTG SKYSNESLKT VLEEWFGDSI LGDLKCPVVI PTIDFTRGSP VTLKTPHNPN LKRDWKLKIV DVALATSAAP T YFPRHPIG ...String:
MEKFQILALS GGGYRGLFTA TVLKELEQEA KENGHDSIAD CFDLITGTSV GGIVALAIAY GIKVEAIVDL FKSHGDKIFQ PKPFLKFTG SKYSNESLKT VLEEWFGDSI LGDLKCPVVI PTIDFTRGSP VTLKTPHNPN LKRDWKLKIV DVALATSAAP T YFPRHPIG PNEYVAGGLF ANDPSLIGLH EADYMFKKNI QDVHILSIGT LSSKKQLNPS TKKDGGYLDW GEGSILKAAP NI IDLVLSS QQQFMEQMVK HRMEPFPNQF YKIDEQIVQA SAQFIGLDET SDAAKQVLEG NGIQSAKVAL GKDFIRNYFN QPS RKREWF DGPQKNV

UniProtKB: UNIPROTKB: A0A9E9MHI8

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 523579
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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