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- EMDB-22077: Cryo-EM Structure of CagX and CagY within the dCag3 Helicobacter ... -

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Basic information

Entry
Database: EMDB / ID: EMD-22077
TitleCryo-EM Structure of CagX and CagY within the dCag3 Helicobacter pylori PR
Map dataHelicobacter pylori T4SS dCag3 PR
Sample
  • Complex: Helicobacter pylori dCag3 Cag T4SS PR
    • Protein or peptide: Cag pathogenicity island protein (Cag8)
    • Protein or peptide: Cag pathogenicity island protein (Cag7)
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) / Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSheedlo MJ / Chung JM / Sawhney N / Durie CL / Cover TL / Ohi MD / Lacy DB
Funding support United States, 7 items
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, 2020-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x6l
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6x6l
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22077.png

Downloads & links

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Map

FileDownload / File: emd_22077.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelicobacter pylori T4SS dCag3 PR
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.026390014 - 0.04184106
Average (Standard dev.)3.5585766e-05 (±0.0011081891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions510510510
Spacing510510510
CellA=B=C: 510.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z510510510
origin x/y/z0.0000.0000.000
length x/y/z510.000510.000510.000
α/β/γ90.00090.00090.000
start NX/NY/NZ212211153
NX/NY/NZ80102186
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-0.0260.0420.000

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Supplemental data

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Sample components

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Entire : Helicobacter pylori dCag3 Cag T4SS PR

EntireName: Helicobacter pylori dCag3 Cag T4SS PR
Components
  • Complex: Helicobacter pylori dCag3 Cag T4SS PR
    • Protein or peptide: Cag pathogenicity island protein (Cag8)
    • Protein or peptide: Cag pathogenicity island protein (Cag7)

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Supramolecule #1: Helicobacter pylori dCag3 Cag T4SS PR

SupramoleculeName: Helicobacter pylori dCag3 Cag T4SS PR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori (bacteria)

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Macromolecule #1: Cag pathogenicity island protein (Cag8)

MacromoleculeName: Cag pathogenicity island protein (Cag8) / type: protein_or_peptide / ID: 1 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695
Molecular weightTheoretical: 60.607324 KDa
SequenceString: MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQLE KDETISYITT GFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT RDYQEFLKTK KLIVDAPDPK ELEEQKKALE KEKEAKEQAQ K AQKDKREK ...String:
MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQLE KDETISYITT GFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT RDYQEFLKTK KLIVDAPDPK ELEEQKKALE KEKEAKEQAQ K AQKDKREK RKEERAKNRA NLENLTNAMS NPQNLSNNKN LSEFIKQQRE NELDQMERLE DMQEQAQANA LKQIEELNKK QA EETIKQR AKDKINIKTD KPQKSPEDNS IELSPSDSAW RTNLVVRTNK ALYQFILRIA QKDNFASAYL TVKLEYPQRH EVS SVIEEL KKREEAKRQK ELIKQENLNT TAYINRVMMA SNEQIINKEK IREEKQKIIL DQAKALETQY VHNALKRNPV PRNY NYYQA PEKRSKHIMP SEIFDDGTFT YFGFKNITLQ PAIFVVQPDG KLSMTDAAID PNMTNSGLRW YRVNEIAEKF KLIKD KALV TVINKGYGKN PLTKNYNIKN YGELERVIKK LPEVRDK

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Macromolecule #2: Cag pathogenicity island protein (Cag7)

MacromoleculeName: Cag pathogenicity island protein (Cag7) / type: protein_or_peptide / ID: 2 / Number of copies: 17 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695
Molecular weightTheoretical: 219.748641 KDa
SequenceString: MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKL FKKARKLVDN KKPFTQQKNL DEETQELNEE DDQENNEYQE ETQTDLIDDE TSKKTQQHSP QDLSNEEATE A NHFENLLK ...String:
MNEENDKLET SKKAQQDSPQ DLSNEEATEA NHFENLLKES KESSDHHLDN PTETQTHFDG DKSEETQTQM DSEGNETSES SNGSLADKL FKKARKLVDN KKPFTQQKNL DEETQELNEE DDQENNEYQE ETQTDLIDDE TSKKTQQHSP QDLSNEEATE A NHFENLLK ESKESSDHHL DNPTETQTNF DGDKSEETQT QMDSEGNETS ESSNGSLADK LFKKARKLVD NKKPFTQQKN LD EETQELN EEDDQENNEY QEETQTDLID DETSKKTQQH SPQDLSNEEA TEANHFENLL KESKESSDHH LDNPTETQTN FDG DKSEEI TDDSNDQEII KGSKKKYIIG GIVVAVLIVI ILFSRSIFHY FMPLEDKSSR FSKDRNLYVN DEIQIRQEYN RLLK ERNEK GNMIDKNLFF NDDPNRTLYN YLNIAEIEDK NPLRAFYECI SNGGNYEECL KLIKDKKLQD QMKKTLEAYN DCIKN AKTE EERIKCLDLI KDENLKKSLL NQQKVQVALD CLKNAKTDEE RNECLKLIND PEIREKFRKE LELQKELQEY KDCIKN AKT EAEKNKCLKG LSKEAIERLK QQALDCLKNA KTDEERNECL KNIPQDLQKE LLADMSVKAY KDCVSKARNE KEKQECE KL LTPEARKKLE QQVLDCLKNA KTDEERKKCL KDLPKDLQSD ILAKESLKAY KDCVSQAKTE AEKKECEKLL TPEAKKLL E EEAKESVKAY LDCVSQAKTE AEKKECEKLL TPEAKKKLEE AKKSVKAYLD CVSRARNEKE KKECEKLLTP EAKKLLEQQ ALDCLKNAKT DKERKKCLKD LPKDLQKKVL AKESVKAYLD CVSQAKTEAE KKECEKLLTP EARKLLEEAK KSVKAYLDCV SQAKTEAEK KECEKLLTPE ARKLLEE(UNK)AK ESVKAYLDCV SQAKNEAEKK ECEKLLTLES KKKLEEAKKS VKAYLDC VS QAKTEAEKKE CEKLLTPEAK KLLEQQALDC LKNAKTEADK KRCVKDLPKD LQKKVLAKES LKAYKDCVSK ARNEKEKK E CEKLLTPEAK KLLEEAKKSV KAYLDCVSQA KTEAEKKECE KLLTPEARKL LEEAKESVKA YKDCVSKARN EKEKKECEK LLTPEAKKLL EQQVLDCLKN AKTEADKKRC VKDLPKDLQK KVLAKESVKA YLDCVSRARN EKEKKECEKL LTPEAKKLLE EAKESLKAY KDCLSQARNE EERRACEKLL TPEARKLLEQ EVKKSIKAYL DCVSRARNEK EKKECEKLLT PEARKFLAKQ V LNCLEKAG NEEERKACLK NLPKDLQENI LAKESLKAYK DCLSQARNEE ERRACEKLLT PEARKLLEQE VKKSVKAYLD CV SRARNEK EKKECEKLLT PEARKFLAKE LQQKDKAIKD CLKNADPNDR AAIMKCLDGL SDEEKLKYLQ EAREKAVADC LAM AKTDEE KRKCQNLYSD LIQEIQNKRT QNKQNQLSKT ERLHQASECL DNLDDPTDQE AIEQCLEGLS DSERALILGI KRQA DEVDL IYSDLRNRKT FDNMAAKGYP LLPMDFKNGG DIATINATNV DADKIASDNP IYASIEPDIA KQYETEKTIK DKNLE AKLA KALGGNKKDD DKEKSKKSTA EAKAENNKID KDVAETAKNI SEIALKNKKE KSGEFVDENG NPIDDKKKAE KQDETS PVK QAFIGKSDPT FVLAQYTPIE ITLTSKVDAT LTGIVSGVVA KDVWNMNGTM ILLDKGTKVY GNYQSVKGGT PIMTRLM IV FTKAITPDGV IIPLANAQAA GMLGEAGVDG YVNNHFMKRI GFAVIASVVN SFLQTAPIIA LDKLIGLGKG RSERTPEF N YALGQAINGS MQSSAQMSNQ ILGQLMNIPP SFYKNEGDSI KILTMDDIDF SGVYDVKITN KSVVDEIIKQ STKTLSREH EEITTSPKGG N

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 59.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10477
FSC plot (resolution estimation)

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