[English] 日本語
Yorodumi
- EMDB-60745: Cryo-EM structure of cUA bound CapE filament -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60745
TitleCryo-EM structure of cUA bound CapE filament
Map data
Sample
  • Complex: CapE
    • Protein or peptide: cUMP-AMP-activated phospholipase
  • Ligand: 3'3'-cUMP-AMP
KeywordsCapE / patatin-like phospholipase protein / LIPID BINDING PROTEIN
Function / homology
Function and homology information


phospholipase A1 / phospholipase A1 activity / lipid catabolic process / fatty acid metabolic process / defense response to virus / membrane
Similarity search - Function
Patatin-like phospholipase domain / Patatin-like phospholipase / Patatin-like phospholipase (PNPLA) domain profile. / Acyl transferase/acyl hydrolase/lysophospholipase
Similarity search - Domain/homology
cUMP-AMP-activated phospholipase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsGao A / Wang JG
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2025
Title: Cyclic-dinucleotide-induced filamentous assembly of phospholipases governs broad CBASS immunity.
Authors: Jingge Wang / Zhao Li / Hao Lang / Wenfeng Fu / Yina Gao / Sen Yin / Panpan Sun / Zhaolong Li / Jiafeng Huang / Songqing Liu / Yun Zhu / Fei Sun / Dong Li / Pu Gao / Ang Gao /
Abstract: Cyclic-oligonucleotide-based antiphage signaling systems (CBASS), a widespread antiviral bacterial immune system homologous to the mammalian cGAS-STING pathway, synthesizes cyclic nucleotide signals ...Cyclic-oligonucleotide-based antiphage signaling systems (CBASS), a widespread antiviral bacterial immune system homologous to the mammalian cGAS-STING pathway, synthesizes cyclic nucleotide signals and triggers effector proteins to induce cell death and prevent viral propagation. Among various CBASS effectors, phospholipase effectors are the first to be discovered and are one of the most widespread families that sense cyclic dinucleotides to degrade cell membrane phospholipids. Here, we report that CBASS phospholipases assemble from a dimeric inactive state into active higher-order filamentous oligomers upon sensing cyclic dinucleotides. Using a combined approach of cryo-electron microscopy and X-ray crystallography, we have determined the structures of CBASS phospholipase in the inactive dimeric state, the cyclic-dinucleotide-bound active higher-order state, and the substrate-analog-bound catalytic mimicry state, thereby visualizing the complete conformational reorganization process. Complemented by functional assays of intermolecular binding, phospholipase enzymatic activity, in vitro membrane disruption, and in vivo antiphage efficiency, our work elucidates the mechanisms of assembly and activation of CBASS phospholipases.
History
DepositionJul 9, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60745.png

Downloads & links

-
Map

FileDownload / File: emd_60745.map.gz / Format: CCP4 / Size: 58.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 248 pix.
= 337.28 Å		1.36 Å/pix.
x 248 pix.
= 337.28 Å		1.36 Å/pix.
x 248 pix.
= 337.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.023
Minimum - Maximum-0.1551653 - 0.21842419
Average (Standard dev.)0.000017562868 (±0.0071523916)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions248248248
Spacing248248248
CellA=B=C: 337.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60745_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60745_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CapE

EntireName: CapE
Components
  • Complex: CapE
    • Protein or peptide: cUMP-AMP-activated phospholipase
  • Ligand: 3'3'-cUMP-AMP

-
Supramolecule #1: CapE

SupramoleculeName: CapE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: cUMP-AMP-activated phospholipase

MacromoleculeName: cUMP-AMP-activated phospholipase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: phospholipase A1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 35.406938 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTYSVSPSSL LTEYGNDNIC RVLALDGGGA KGFYTLGVLK EIEAMLGCPL YKRFDLVFGT STGAIIAALI ALGYEVDQIH ALYTEHVPR VMSSRSAAAR TMALQDLAKE VFQDKTFEDV LMGIGIVATR WMTERPMIFK GNVVQAHGRK GTFSPGFGVS I ADAVQASC ...String:
MTYSVSPSSL LTEYGNDNIC RVLALDGGGA KGFYTLGVLK EIEAMLGCPL YKRFDLVFGT STGAIIAALI ALGYEVDQIH ALYTEHVPR VMSSRSAAAR TMALQDLAKE VFQDKTFEDV LMGIGIVATR WMTERPMIFK GNVVQAHGRK GTFSPGFGVS I ADAVQASC SAYPFFERKV IVTAAGDKVE LIDGGYCANN PTLFAIADAT VALKKDHKDI RVINVGVGIY PEPKPGLLMR IA KKWLAVQ LLQKTLEINT QSMDQLRDIL FKDIPTIRIS DTFERPEMAT DLLEYNLDKL NTLRQRGRES FGAREAQLRE FLI

UniProtKB: cUMP-AMP-activated phospholipase

-
Macromolecule #2: 3'3'-cUMP-AMP

MacromoleculeName: 3'3'-cUMP-AMP / type: ligand / ID: 2 / Number of copies: 4 / Formula: A1AEP
Molecular weightTheoretical: 635.372 Da

-
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 K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 249892
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
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