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- EMDB-20024: Cryo-EM structure of Helicobacter pylori VacA hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-20024
TitleCryo-EM structure of Helicobacter pylori VacA hexamer
Map dataCryo-EM structure of Helicobacter pylori VacA hexamer
Sample
  • Complex: Vacuolating cytotoxin A
    • Protein or peptide: Vacuolating cytotoxin autotransporter
KeywordsVacA / TOXIN
Function / homology
Function and homology information


cell outer membrane / toxin activity / periplasmic space / cell surface / extracellular region
Similarity search - Function
Vacuolating cytotoxin / Vacuolating cyotoxin / Outer membrane autotransporter barrel / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily
Similarity search - Domain/homology
Vacuolating cytotoxin autotransporter
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsErwin AL / Cover TL
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI039657 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA116087 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM08230 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118089 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32CA119925 United States
Other government5I01BX000627 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31AI112324 United States
CitationJournal: J Mol Biol / Year: 2019
Title: Cryo-EM Analysis Reveals Structural Basis of Helicobacter pylori VacA Toxin Oligomerization.
Authors: Min Su / Amanda L Erwin / Anne M Campbell / Tasia M Pyburn / Lauren E Salay / Jessica L Hanks / D Borden Lacy / David L Akey / Timothy L Cover / Melanie D Ohi /
Abstract: Helicobacter pylori colonizes the human stomach and contributes to the development of gastric cancer and peptic ulcer disease. H. pylori secretes a pore-forming toxin called vacuolating cytotoxin A ...Helicobacter pylori colonizes the human stomach and contributes to the development of gastric cancer and peptic ulcer disease. H. pylori secretes a pore-forming toxin called vacuolating cytotoxin A (VacA), which contains two domains (p33 and p55) and assembles into oligomeric structures. Using single-particle cryo-electron microscopy, we have determined low-resolution structures of a VacA dodecamer and heptamer, as well as a 3.8-Å structure of the VacA hexamer. These analyses show that VacA p88 consists predominantly of a right-handed beta-helix that extends from the p55 domain into the p33 domain. We map the regions of p33 and p55 involved in hexamer assembly, model how interactions between protomers support heptamer formation, and identify surfaces of VacA that likely contact membrane. This work provides structural insights into the process of VacA oligomerization and identifies regions of VacA protomers that are predicted to contact the host cell surface during channel formation.
History
DepositionMar 27, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.33
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6ody
  • Surface level: 4.33
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20024.png

Downloads & links

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Map

FileDownload / File: emd_20024.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Helicobacter pylori VacA hexamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å		1.25 Å/pix.
x 320 pix.
= 400. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.33 / Movie #1: 4.33
Minimum - Maximum-5.5403633 - 19.006388000000001
Average (Standard dev.)0.0026760583 (±0.9157963)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z400.000400.000400.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-5.54019.0060.003

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Supplemental data

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Sample components

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Entire : Vacuolating cytotoxin A

EntireName: Vacuolating cytotoxin A
Components
  • Complex: Vacuolating cytotoxin A
    • Protein or peptide: Vacuolating cytotoxin autotransporter

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Supramolecule #1: Vacuolating cytotoxin A

SupramoleculeName: Vacuolating cytotoxin A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Hexamer
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: s1/i1/m1
Molecular weightTheoretical: 528 KDa

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Macromolecule #1: Vacuolating cytotoxin autotransporter

MacromoleculeName: Vacuolating cytotoxin autotransporter / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria) / Strain: s1/i1/m1
Molecular weightTheoretical: 70.392578 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)QPTQVID GPFAGGKDTV VNIDRINTKA DGTIKVGGFK ASLTTNAAHL NIGKGGVN L SNQASGRTLL VENLTGNITV DGPLRVNNQV GGYALAGSSA NFEFKAGVDT KNGTATFNND ISLGRFVNLK VDAHTANFK GIDTGNGGFN TLDFSGVTNK VNINKLITAS TNVAVKNFNI NELIVKTNGV SVGEYTHFSE DIGSQSRINT VRLETGTRSI FSGGVKFKS GEKLVIDEFY YSPWNYFDAR NIKNVEITRK FASSTPENPW GTSKLMFNNL TLGQNAVMDY SQFSNLTIQG D FINNQGTI NYLVRGGKVA TLNVGNAAAM MFNNDIDSAT GFYKPLIKIN SAQDLIKNTE HVLLKAKIIG YGNVSTGTNG IS NVNLEEQ FKERLALYNN NNRMDTCVVR NTDDIKACGM AIGNQSMVNN PDNYKYLIGK AWKNIGISKT ANGSKISVYY LGN STPTEN GGNTTNLPTN T

UniProtKB: Vacuolating cytotoxin autotransporter

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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: 8
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: 48.0 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

Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133827
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING

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