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- EMDB-62576: Cryo-EM structure of CtpA from Helicobacter pylori in conformation II -

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Basic information

Entry
Database: EMDB / ID: EMD-62576
TitleCryo-EM structure of CtpA from Helicobacter pylori in conformation II
Map data
Sample
  • Complex: Carboxyl-terminal processing protease CtpA from Helicobacter pylori
    • Protein or peptide: Carboxyl-terminal protease
KeywordsCarboxyl-terminal processing protease / CtpA / HYDROLASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsSun K / Zhang H / Au SWN
Funding support Hong Kong, 1 items
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 conformation II
Authors: Sun K / Zhang H / Au SWN
History
DepositionDec 3, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62576.png

Downloads & links

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Map

FileDownload / File: emd_62576.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 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: 0.177
Minimum - Maximum-1.2809871 - 2.2489414
Average (Standard dev.)0.0012344911 (±0.05075583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_62576_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_62576_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Carboxyl-terminal processing protease CtpA from Helicobacter pylori

EntireName: Carboxyl-terminal processing protease CtpA from Helicobacter pylori
Components
  • Complex: Carboxyl-terminal processing protease CtpA from Helicobacter pylori
    • Protein or peptide: Carboxyl-terminal protease

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Supramolecule #1: Carboxyl-terminal processing protease CtpA from Helicobacter pylori

SupramoleculeName: Carboxyl-terminal processing protease CtpA from Helicobacter pylori
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori G27 (bacteria)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: Carboxyl-terminal protease

MacromoleculeName: Carboxyl-terminal protease / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori G27 (bacteria) / Strain: G27
Molecular weightTheoretical: 46.118207 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHMFS RFSNVVSEIE KKYVDKISIS EIMTKAIEGL LSNLDAHSAY LNEKKFKEFQ AQTEGEFGGL GITVGMRDGV LTVIAPLEG TPAYKAGVKS GDNILKINNE STLSMSIDDA INLMRGKPKT PIQITIVRKN EPKPLVFNII RDIIKLPSVY V KKIKETPY ...String:
MHHHHHHMFS RFSNVVSEIE KKYVDKISIS EIMTKAIEGL LSNLDAHSAY LNEKKFKEFQ AQTEGEFGGL GITVGMRDGV LTVIAPLEG TPAYKAGVKS GDNILKINNE STLSMSIDDA INLMRGKPKT PIQITIVRKN EPKPLVFNII RDIIKLPSVY V KKIKETPY LYVRVSGFDK NVTKSVLEGL KANPKAKGIV LDLRGNPGGL LNQAVGLSNL FIKEGVLVSQ KGKNKEESLE YK ANGRAPY TNLPIAVLVN GGSASASEIV AGALQDHKRA VIIGEKTFGK GSVQMLLPVN KDEAIKITTA RYYLPSGRTI QAK GITPDI VIYPGKVPEN ENKFSLKEAD LKHHLEQELK KLDDKTPNSK EADKDKKNEE EKEVTPKMIN DDIQLKTAID SLKT WSIVD EKMDEKAPKK K

UniProtKB: Carboxyl-terminal protease

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 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: PDB ENTRY
PDB model - PDB ID:

9jr1

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133262
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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