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- PDB-9ksp: Cryo-EM structure of CtpA from Helicobacter pylori in an all-rest... -

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Basic information

Entry
Database: PDB / ID: 9ksp
TitleCryo-EM structure of CtpA from Helicobacter pylori in an all-resting state
ComponentsCarboxyl-terminal protease
KeywordsHYDROLASE / Carboxyl-terminal processing protease / CtpA / Helicobacter pylori
Function / homology
Function and homology information


serine-type peptidase activity / outer membrane-bounded periplasmic space / endopeptidase activity / signal transduction / proteolysis
Similarity search - Function
C-terminal-processing peptidase S41A / tail specific protease / Tail specific protease / Peptidase family S41 / PDZ domain 6 / PDZ domain / ClpP/crotonase-like domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily
Similarity search - Domain/homology
Carboxyl-terminal protease
Similarity search - Component
Biological speciesHelicobacter pylori G27 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsSun, K. / Zhang, H. / Au, S.W.N.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)14117622 Hong Kong
CitationJournal: To Be Published
Title: Cryo-EM structure of CtpA from Helicobacter pylori in an all-resting state
Authors: Sun, K. / Zhang, H. / Au, S.W.N.
History
DepositionNov 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Carboxyl-terminal protease
A: Carboxyl-terminal protease
B: Carboxyl-terminal protease
D: Carboxyl-terminal protease
E: Carboxyl-terminal protease
F: Carboxyl-terminal protease


Theoretical massNumber of molelcules
Total (without water)276,7096
Polymers276,7096
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Carboxyl-terminal protease


Mass: 46118.207 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori G27 (bacteria) / Strain: G27 / Gene: HPG27_1298 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B5Z8Z7
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: Carboxyl-terminal processing protease CtpA from Helicobacter pylori
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.28 MDa / Experimental value: YES
Source (natural)Organism: Helicobacter pylori G27 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
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: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 144375 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315529
ELECTRON MICROSCOPYf_angle_d0.57320919
ELECTRON MICROSCOPYf_dihedral_angle_d5.9752135
ELECTRON MICROSCOPYf_chiral_restr0.0452474
ELECTRON MICROSCOPYf_plane_restr0.0042629

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