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- EMDB-62384: Cryo-EM Structure of CdnG-E2 complex with GTP from Serratia marcescens -

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Basic information

Entry
Database: EMDB / ID: EMD-62384
TitleCryo-EM Structure of CdnG-E2 complex with GTP from Serratia marcescens
Map data
Sample
  • Complex: CdnG-E2 complex with GTP
    • Protein or peptide: CdnG
    • Protein or peptide: E2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
KeywordscGAS / CdnG / E2 / CBASS / ANTIVIRAL PROTEIN
Biological speciesSerratia marcescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsXiao J / Wang L / Wang Z
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: mLife / Year: 2026
Title: Structures and mechanism of E2-CBASS anti-phage system.
Authors: Jun Xiao / Yan Yan / Jing Li / Greater Kayode Oyejobi / Dongyang Lan / Bin Zhu / Zhiming Wang / Longfei Wang /
Abstract: Bacteria deploy diverse innate immune systems to combat bacteriophage infections. The cyclic-oligonucleotide-based anti-phage signaling system (CBASS) is a type of innate prokaryotic immune system. ...Bacteria deploy diverse innate immune systems to combat bacteriophage infections. The cyclic-oligonucleotide-based anti-phage signaling system (CBASS) is a type of innate prokaryotic immune system. CBASS synthesizes cyclic-oligonucleotide through cGAS/DncV-like nucleotidyltransferases (CD-NTases) to activate downstream effectors, which kill bacteriophage-infected bacteria, thereby stopping phage spread. One major class of CBASS contains a homolog of eukaryotic ubiquitin-conjugating enzymes, either as an E1-E2 fusion or a single E2 enzyme. Both enzymes function by regulating CD-NTase activity. Currently, many structures of CD-NTases have been reported, but there are only a few reports of structures where CD-NTases form complexes with the associated E2. In this study, we analyzed the length and classification of the CD-NTase in two types of type II CBASS-E1E2/JAB-CBASS and E2-CBASS. We found that the CD-NTase in E2-CBASS is longer and predominantly belongs to clade G. We also present the structure of the CdnG-E2 complex with the bound GTP substrate, which indicates the conservation of the donor binding pattern. Interestingly, we discovered that CdnG contains a conserved C-terminal α-helix and β-sheet structure, which is uniquely involved in forming a complex with E2. We also found that the structure of the E2 protein in the E2-CBASS system is highly conserved. Altogether, we provide mechanistic insights into the E2-CBASS system.
History
DepositionNov 13, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62384.png

Downloads & links

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Map

FileDownload / File: emd_62384.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 360 pix.
= 343.04 Å		0.95 Å/pix.
x 360 pix.
= 343.04 Å		0.95 Å/pix.
x 360 pix.
= 343.04 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95289 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0722
Minimum - Maximum-0.93619925 - 1.2886956
Average (Standard dev.)-0.00012454347 (±0.0104259625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 343.04004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62384_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62384_half_map_2.map
Projections & Slices
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Sample components

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Entire : CdnG-E2 complex with GTP

EntireName: CdnG-E2 complex with GTP
Components
  • Complex: CdnG-E2 complex with GTP
    • Protein or peptide: CdnG
    • Protein or peptide: E2
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: CdnG-E2 complex with GTP

SupramoleculeName: CdnG-E2 complex with GTP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Serratia marcescens (bacteria)

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Macromolecule #1: CdnG

MacromoleculeName: CdnG / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia marcescens (bacteria)
Molecular weightTheoretical: 45.481707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYGSTTARNL PSGKKQRIAD LLSQIIETLD LTKTQYANIE SAYNGVGTFL SEGDDPLLQD AVIYPQGSVR LNTTVKPKNE EQYDIDLIC YLPHATQADY TGVISAIRQR LESHKTYKTL LSELPRGFRI NYAGDYHLDI TPGRDHTGTA HPGQPLWVVD A QTAWKESN ...String:
MYGSTTARNL PSGKKQRIAD LLSQIIETLD LTKTQYANIE SAYNGVGTFL SEGDDPLLQD AVIYPQGSVR LNTTVKPKNE EQYDIDLIC YLPHATQADY TGVISAIRQR LESHKTYKTL LSELPRGFRI NYAGDYHLDI TPGRDHTGTA HPGQPLWVVD A QTAWKESN PSGYAEWFES SASVQPLRTI LVMDSASRVG TEALLPLPDS TDKKLLNHIV QILKRHRDEW AAEQDEVRQR CR PISVIIT TLACHAYNHI IADRRAYDND LDILLDVLEL MPDFIVSTQG AIHVNNPHMP EENFAEKWNR SEQDEGPQRS EAF YQWHAA AQATFNTIAA SVGEDNLFLS LEDSFGKTPV DVVRQRLMEH MQSAREQGSL HLDKKTGGLI ATGLAGTAAQ AGVP KNTFY GE

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Macromolecule #2: E2

MacromoleculeName: E2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia marcescens (bacteria)
Molecular weightTheoretical: 18.78267 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNNVVIRHHC KPLTIAQQYR ALKAGGPYER LRIIHHDRTL LWEGWLQPSL FSRRYKVAVR YSLGTPPICV VTEPDLFALA GTRAIPHLY PADKHIPGAR LCLFLPRSQA DDGLSEWRAQ LKISDTLIPW ASLWLFYFEQ WLHTGHWEGG GKHPRPSEVK N ER

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 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: 1.1 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: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 349606
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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