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- EMDB-20023: Reconstruction of a T4SS OMCC -

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Basic information

Entry
Database: EMDB / ID: EMD-20023
TitleReconstruction of a T4SS OMCC
Map dataReconstruction of a T4SS OMCC using C1
Sample
  • Complex: Reconstruction of a proposed asymmetric unit from an H. pylori OMCC
Function / homology
Function and homology information


outer membrane / protein secretion / membrane => GO:0016020 / membrane / plasma membrane
Similarity search - Function
Cag pathogenicity island protein Cag12 / Cag pathogenicity island protein Cag12 / 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 ...Cag pathogenicity island protein Cag12 / Cag pathogenicity island protein Cag12 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Type IV secretion system apparatus protein CagY / Type IV secretion system apparatus protein CagX / Cag pathogenicity island protein (Cag7) / CAG pathogenicity island protein 12 / Cag pathogenicity island protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsChung JM / Sheedlo MJ / Campbell AM / Sawhney N / Frick-Cheng AE / Lacy DB / Cover TL / Ohi MD
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesNIH AI118932 United States
National Institutes of Health/National Institute of General Medical SciencesGM103310 United States
National Institutes of Health/National Cancer InstituteCA116087 United States
Other government1I01BX004447 United States
CitationJournal: Elife / Year: 2019
Title: Structure of the Cag type IV secretion system.
Authors: Jeong Min Chung / Michael J Sheedlo / Anne M Campbell / Neha Sawhney / Arwen E Frick-Cheng / Dana Borden Lacy / Timothy L Cover / Melanie D Ohi /
Abstract: Bacterial type IV secretion systems (T4SSs) are molecular machines that can mediate interbacterial DNA transfer through conjugation and delivery of effector molecules into host cells. The Cag T4SS ...Bacterial type IV secretion systems (T4SSs) are molecular machines that can mediate interbacterial DNA transfer through conjugation and delivery of effector molecules into host cells. The Cag T4SS translocates CagA, a bacterial oncoprotein, into gastric cells, contributing to gastric cancer pathogenesis. We report the structure of a membrane-spanning Cag T4SS assembly, which we describe as three sub-assemblies: a 14-fold symmetric outer membrane core complex (OMCC), 17-fold symmetric periplasmic ring complex (PRC), and central stalk. Features that differ markedly from those of prototypical T4SSs include an expanded OMCC and unexpected symmetry mismatch between the OMCC and PRC. This structure is one of the largest bacterial secretion system assemblies ever reported and illustrates the remarkable structural diversity that exists among bacterial T4SSs.
History
DepositionMar 26, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 3, 2019-
UpdateOct 7, 2020-
Current statusOct 7, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.69
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.69
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20023.png

Downloads & links

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Map

FileDownload / File: emd_20023.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of a T4SS OMCC using C1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 510 pix.
= 836.4 Å		1.64 Å/pix.
x 510 pix.
= 836.4 Å		1.64 Å/pix.
x 510 pix.
= 836.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.69 / Movie #1: 0.69
Minimum - Maximum-1.4341307 - 3.1059096
Average (Standard dev.)0.0033102506 (±0.108116955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 836.39996 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z510510510
origin x/y/z0.0000.0000.000
length x/y/z836.400836.400836.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ162182277
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-1.4343.1060.003

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Supplemental data

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Sample components

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Entire : Reconstruction of a proposed asymmetric unit from an H. pylori OMCC

EntireName: Reconstruction of a proposed asymmetric unit from an H. pylori OMCC
Components
  • Complex: Reconstruction of a proposed asymmetric unit from an H. pylori OMCC

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Supramolecule #1: Reconstruction of a proposed asymmetric unit from an H. pylori OMCC

SupramoleculeName: Reconstruction of a proposed asymmetric unit from an H. pylori OMCC
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Helicobacter pylori (bacteria)

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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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 59.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 24662
CTF correctionSoftware - Name: Gctf
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 17605
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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