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- EMDB-20020: Reconstruction of a T4SS OMCC -

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Basic information

Entry
Database: EMDB / ID: EMD-20020
TitleReconstruction of a T4SS OMCC
Map dataC14 Reconstruction of T4SS OMCC
Sample
  • Complex: Type IV secretion system apparatus protein CagY
    • Protein or peptide: Type IV secretion system apparatus protein CagY
KeywordsT4SS / Secretion / H. pylori / TRANSLOCASE
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: 3.8 Å
AuthorsChung JM / Sheedlo MJ
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)NIH AI118932 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)GM103310 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-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.027
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6odi
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6oee
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6oef
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6oeg
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6oeh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20020.png

Downloads & links

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Map

FileDownload / File: emd_20020.map.gz / Format: CCP4 / Size: 506 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC14 Reconstruction of T4SS OMCC
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: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.067185566 - 0.13557947
Average (Standard dev.)0.00007303039 (±0.004183618)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS510510510
D min/max/mean-0.0670.1360.000

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Supplemental data

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Sample components

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Entire : Type IV secretion system apparatus protein CagY

EntireName: Type IV secretion system apparatus protein CagY
Components
  • Complex: Type IV secretion system apparatus protein CagY
    • Protein or peptide: Type IV secretion system apparatus protein CagY

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Supramolecule #1: Type IV secretion system apparatus protein CagY

SupramoleculeName: Type IV secretion system apparatus protein CagY / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Helicobacter pylori (bacteria)

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Macromolecule #1: Type IV secretion system apparatus protein CagY

MacromoleculeName: Type IV secretion system apparatus protein CagY / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Helicobacter pylori (bacteria)
Molecular weightTheoretical: 219.792656 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 ARKLLEEEAK ESVKAYLDCV SQAKNEAEKK ECEKLLTLES KKKLEEAKKS VKAYLDCVSQ A KTEAEKKE CEKLLTPEAK KLLEQQALDC LKNAKTEADK KRCVKDLPKD LQKKVLAKES LKAYKDCVSK ARNEKEKKEC EK LLTPEAK KLLEEAKKSV KAYLDCVSQA KTEAEKKECE KLLTPEARKL LEEAKESVKA YKDCVSKARN EKEKKECEKL LTP EAKKLL EQQVLDCLKN AKTEADKKRC VKDLPKDLQK KVLAKESVKA YLDCVSRARN EKEKKECEKL LTPEAKKLLE EAKE SLKAY KDCLSQARNE EERRACEKLL TPEARKLLEQ EVKKSIKAYL DCVSRARNEK EKKECEKLLT PEARKFLAKQ VLNCL EKAG NEEERKACLK NLPKDLQENI LAKESLKAYK DCLSQARNEE ERRACEKLLT PEARKLLEQE VKKSVKAYLD CVSRAR NEK EKKECEKLLT PEARKFLAKE LQQKDKAIKD CLKNADPNDR AAIMKCLDGL SDEEKLKYLQ EAREKAVADC LAMAKTD EE KRKCQNLYSD LIQEIQNKRT QNKQNQLSKT ERLHQASECL DNLDDPTDQE AIEQCLEGLS DSERALILGI KRQADEVD L IYSDLRNRKT FDNMAAKGYP LLPMDFKNGG DIATINATNV DADKIASDNP IYASIEPDIA KQYETEKTIK DKNLEAKLA KALGGNKKDD DKEKSKKSTA EAKAENNKID KDVAETAKNI SEIALKNKKE KSGEFVDENG NPIDDKKKAE KQDETSPVKQ AFIGKSDPT FVLAQYTPIE ITLTSKVDAT LTGIVSGVVA KDVWNMNGTM ILLDKGTKVY GNYQSVKGGT PIMTRLMIVF T KAITPDGV IIPLANAQAA GMLGEAGVDG YVNNHFMKRI GFAVIASVVN SFLQTAPIIA LDKLIGLGKG RSERTPEFNY AL GQAINGS MQSSAQMSNQ ILGQLMNIPP SFYKNEGDSI KILTMDDIDF SGVYDVKITN KSVVDEIIKQ STKTLSREHE EIT TSPKGG N

UniProtKB: Type IV secretion system apparatus protein CagY

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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
GridMaterial: COPPER / Mesh: 400
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
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C14 (14 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 17159
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 68.95
Output model

PDB-6odi:
Structure of CagY from a cryo-EM reconstruction of a T4SS

PDB-6oee:
Structure of CagT from a cryo-EM reconstruction of a T4SS

PDB-6oef:
PolyAla Model of the O-layer from the Type 4 Secretion System of H. pylori

PDB-6oeg:
Structure of CagX from a cryo-EM reconstruction of a T4SS

PDB-6oeh:
PolyAla Model of OMCC I-Layer

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