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- PDB-9kkb: Cryo-EM Structure of CdnG-E2 complex with GTP from Serratia marcescens -

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Basic information

Entry
Database: PDB / ID: 9kkb
TitleCryo-EM Structure of CdnG-E2 complex with GTP from Serratia marcescens
Components
  • CdnG
  • E2
KeywordsANTIVIRAL PROTEIN / cGAS / CdnG / E2 / CBASS
Function / homologyGUANOSINE-5'-TRIPHOSPHATE
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsXiao, J. / Wang, L. / Wang, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mlife / Year: 2025
Title: Cryo-EM Structure of CdnG-E2 complex with GTP from Serratia marcescens
Authors: Xiao, J. / Wang, L.
History
DepositionNov 13, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CdnG
B: E2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7883
Polymers64,2642
Non-polymers5231
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein CdnG


Mass: 45481.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein E2


Mass: 18782.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CdnG-E2 complex with GTP / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Serratia marcescens (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1100 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 349606 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0074399
ELECTRON MICROSCOPYf_angle_d1.3585993
ELECTRON MICROSCOPYf_dihedral_angle_d11.729594
ELECTRON MICROSCOPYf_chiral_restr0.075651
ELECTRON MICROSCOPYf_plane_restr0.011771

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