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- PDB-6x6j: Cryo-EM Structure of CagX and CagY within the Helicobacter pylori PR -

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Basic information

Entry
Database: PDB / ID: 6x6j
TitleCryo-EM Structure of CagX and CagY within the Helicobacter pylori PR
Components
  • Cag pathogenicity island protein (Cag7)
  • Cag pathogenicity island protein (Cag8)
KeywordsPROTEIN TRANSPORT / Helicobacter / T4SS / Secretion
Function / homology
Function and homology information


CagY type 1 repeat / CagY type 1 repeat / DC-EC / DC-EC Repeat / Type IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10/TrbI ...CagY type 1 repeat / CagY type 1 repeat / DC-EC / DC-EC Repeat / Type IV secretion system CagX conjugation protein / Conjugal transfer, TrbG/VirB9/CagX / VirB9/CagX/TrbG, C-terminal / VirB9/CagX/TrbG, C-terminal domain superfamily / Conjugal transfer protein / Type IV secretion system, VirB10/TrbI / Bacterial conjugation TrbI-like protein / Type IV secretion system, VirB10 / TraB / TrbI
Similarity search - Domain/homology
Cag pathogenicity island protein (Cag7) / Cag pathogenicity island protein (Cag8)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSheedlo, M.J. / Chung, J.M. / Sawhney, N. / Durie, C.L. / Cover, T.L. / Ohi, M.D. / Lacy, D.B.
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI118932 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA116087 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI039657 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)2T32DK007673 United States
National Institutes of Health/Office of the DirectorS10OD020011 United States
Other government1I01BX004447 United States
CitationJournal: Elife / Year: 2020
Title: Cryo-EM reveals species-specific components within the Cag type IV secretion system core complex.
Authors: Michael J Sheedlo / Jeong Min Chung / Neha Sawhney / Clarissa L Durie / Timothy L Cover / Melanie D Ohi / D Borden Lacy /
Abstract: The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core ...The pathogenesis of -associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). The Cag T4SS includes a large membrane-spanning core complex containing five proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of the T4SS core complex is dependent on incorporation of interwoven species-specific components.
History
DepositionMay 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
AX: Cag pathogenicity island protein (Cag8)
BX: Cag pathogenicity island protein (Cag8)
CX: Cag pathogenicity island protein (Cag8)
DX: Cag pathogenicity island protein (Cag8)
EX: Cag pathogenicity island protein (Cag8)
FX: Cag pathogenicity island protein (Cag8)
GX: Cag pathogenicity island protein (Cag8)
HX: Cag pathogenicity island protein (Cag8)
IX: Cag pathogenicity island protein (Cag8)
JX: Cag pathogenicity island protein (Cag8)
KX: Cag pathogenicity island protein (Cag8)
LX: Cag pathogenicity island protein (Cag8)
MX: Cag pathogenicity island protein (Cag8)
NX: Cag pathogenicity island protein (Cag8)
OX: Cag pathogenicity island protein (Cag8)
PX: Cag pathogenicity island protein (Cag8)
QX: Cag pathogenicity island protein (Cag8)
AY: Cag pathogenicity island protein (Cag7)
BY: Cag pathogenicity island protein (Cag7)
CY: Cag pathogenicity island protein (Cag7)
DY: Cag pathogenicity island protein (Cag7)
EY: Cag pathogenicity island protein (Cag7)
FY: Cag pathogenicity island protein (Cag7)
GY: Cag pathogenicity island protein (Cag7)
HY: Cag pathogenicity island protein (Cag7)
IY: Cag pathogenicity island protein (Cag7)
JY: Cag pathogenicity island protein (Cag7)
KY: Cag pathogenicity island protein (Cag7)
LY: Cag pathogenicity island protein (Cag7)
MY: Cag pathogenicity island protein (Cag7)
NY: Cag pathogenicity island protein (Cag7)
OY: Cag pathogenicity island protein (Cag7)
PY: Cag pathogenicity island protein (Cag7)
QY: Cag pathogenicity island protein (Cag7)


Theoretical massNumber of molelcules
Total (without water)4,766,05134
Polymers4,766,05134
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area203550 Å2
ΔGint-1016 kcal/mol
Surface area198940 Å2

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Components

#1: Protein
Cag pathogenicity island protein (Cag8)


Mass: 60607.324 Da / Num. of mol.: 17 / Source method: isolated from a natural source
Source: (natural) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / References: UniProt: O25263
#2: Protein
Cag pathogenicity island protein (Cag7)


Mass: 219748.641 Da / Num. of mol.: 17 / Source method: isolated from a natural source
Source: (natural) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / References: UniProt: O25262

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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: Helicobacter pylori Cag T4SS PR / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Helicobacter pylori (bacteria)
Buffer solutionpH: 7
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 59.2 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20929 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 95.94 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006141242
ELECTRON MICROSCOPYf_angle_d0.562155709
ELECTRON MICROSCOPYf_chiral_restr0.04316375
ELECTRON MICROSCOPYf_plane_restr0.00267191
ELECTRON MICROSCOPYf_dihedral_angle_d15.14185406

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