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Open data
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Basic information
Entry | ![]() | ||||||||||||
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Title | Cryo-EM Structure of the Helicobacter pylori CagYdAP OMC | ||||||||||||
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![]() | T4SS / protein translocation / MEMBRANE PROTEIN | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||
![]() | Roberts JR | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Subdomains of the Cag T4SS outer membrane core complex exhibit structural independence. Authors: Jacquelyn R Roberts / Sirena C Tran / Arwen E Frick-Cheng / Kaeli N Bryant / Chiamaka D Okoye / W Hayes McDonald / Timothy L Cover / Melanie D Ohi / ![]() Abstract: The Cag type IV secretion system (Cag T4SS) has an important role in the pathogenesis of gastric cancer. The Cag T4SS outer membrane core complex (OMCC) is organized into three regions: a 14-fold ...The Cag type IV secretion system (Cag T4SS) has an important role in the pathogenesis of gastric cancer. The Cag T4SS outer membrane core complex (OMCC) is organized into three regions: a 14-fold symmetric outer membrane cap (OMC) composed of CagY, CagX, CagT, CagM, and Cag3; a 17-fold symmetric periplasmic ring (PR) composed of CagY and CagX; and a stalk with unknown composition. We investigated how CagT, CagM, and a conserved antenna projection (AP) region of CagY contribute to the structural organization of the OMCC. Single-particle cryo-EM analyses showed that complexes purified from Δ or Δ mutants no longer had organized OMCs, but the PRs remained structured. OMCCs purified from a CagY antenna projection mutant (CagYAP) were structurally similar to WT OMCCs, except for the absence of the α-helical antenna projection. These results indicate that CagY and CagX are sufficient for maintaining a stable PR, but the organization of the OMC requires CagY, CagX, CagM, and CagT. Our results highlight an unexpected structural independence of two major subdomains of the Cag T4SS OMCC. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 979.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.6 KB 18.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.5 KB | Display | ![]() |
Images | ![]() | 191.4 KB | ||
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() | 962.8 MB 962.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 30.4 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_42290_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_42290_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Helicobacter pylori CagYdAP OMC
Entire | Name: Helicobacter pylori CagYdAP OMC |
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Components |
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-Supramolecule #1: Helicobacter pylori CagYdAP OMC
Supramolecule | Name: Helicobacter pylori CagYdAP OMC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Type IV secretion system apparatus protein Cag3
Macromolecule | Name: Type IV secretion system apparatus protein Cag3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MFRKLATAVS LIGLLTSNTL YAKEISEADK VIKATKETKE TKKEAKRLKK EAKQRQQIPD HKKPQYVSV DDTKTQALFD IYDTLNVNDK SFGDWFGNSA LKDKTYLYAM DLLDYNNYLS I ENPIIKTR AMGTYADLII ITGSLEQVNG YYNILKALNK RNAKFVLKIN ...String: MFRKLATAVS LIGLLTSNTL YAKEISEADK VIKATKETKE TKKEAKRLKK EAKQRQQIPD HKKPQYVSV DDTKTQALFD IYDTLNVNDK SFGDWFGNSA LKDKTYLYAM DLLDYNNYLS I ENPIIKTR AMGTYADLII ITGSLEQVNG YYNILKALNK RNAKFVLKIN ENMPYAQATF LR VPKRSDP NAHTLDKGAS IDENKLFEQQ KKMYFNYAND VICRPDDEVC SPLRDEMVAM PTS DSVTQK PNIIAPYSLY RLKETNNANE AQPSPYATQT APENSKEKLI EELIANSQLV ANEE EREKK LLAEKEKQEA ELAKYKLKDL ENQKKLKALE AELKKKNAKK PRVVEVPVSP QTSNS DETM RVVKEKENYN GLLVDKETTI KRSYEGTLIS ENSYSKKTPL NPNDLRSLEE EIKSYY IKS NGLCYTNGIN LYVKIKNDPY KEGMLCGYES VQNLLSPLKD KLKYDKQKLQ KALLKDS K |
-Macromolecule #2: Type IV secretion system apparatus protein CagM
Macromolecule | Name: Type IV secretion system apparatus protein CagM / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MLAKIVFSSL VAFGVLSAN V EQFGSFFN EI KKEQEEV AAK EDALKA RKKL LNNTH DFLED LIFR KQKIKE LMD HRAKVLS DL ENKYKKEK E ALEKETRGK ILTAKSKAYG DLEQALKDN P LYRKLLPN PY AYVLNQE TFT KEDRER LSYY YPQVK ...String: MLAKIVFSSL VAFGVLSAN V EQFGSFFN EI KKEQEEV AAK EDALKA RKKL LNNTH DFLED LIFR KQKIKE LMD HRAKVLS DL ENKYKKEK E ALEKETRGK ILTAKSKAYG DLEQALKDN P LYRKLLPN PY AYVLNQE TFT KEDRER LSYY YPQVK TSSIF KKTT ATTKDK AQA LLQMGVF SL DEEQNKKA S RLALSYKQA IEEYSNNVSN LLSRKELDN I DYYLQLER NK FDSKAKD IAQ KATNTL IFNS ERLAF SMAID KINE KYLRGY EAF SNLLKNV KD DVELNTLT K NFTNQKLSF AQKQKLCLLV LDSFNFDTQ S KKSILKKT NE YNIFVDS DPM MSDKTT MQKE HYKIF NFFKT VVSA YRNNVA KNN PFE |
-Macromolecule #3: Type IV secretion system apparatus protein CagT
Macromolecule | Name: Type IV secretion system apparatus protein CagT / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MLAKIVFSSL VAFGVLSAN V EQFGSFFN EI KKEQEEV AAK EDALKA RKKL LNNTH DFLED LIFR KQKIKE LMD HRAKVLS DL ENKYKKEK E ALEKETRGK ILTAKSKAYG DLEQALKDN P LYRKLLPN PY AYVLNQE TFT KEDRER LSYY YPQVK ...String: MLAKIVFSSL VAFGVLSAN V EQFGSFFN EI KKEQEEV AAK EDALKA RKKL LNNTH DFLED LIFR KQKIKE LMD HRAKVLS DL ENKYKKEK E ALEKETRGK ILTAKSKAYG DLEQALKDN P LYRKLLPN PY AYVLNQE TFT KEDRER LSYY YPQVK TSSIF KKTT ATTKDK AQA LLQMGVF SL DEEQNKKA S RLALSYKQA IEEYSNNVSN LLSRKELDN I DYYLQLER NK FDSKAKD IAQ KATNTL IFNS ERLAF SMAID KINE KYLRGY EAF SNLLKNV KD DVELNTLT K NFTNQKLSF AQKQKLCLLV LDSFNFDTQ S KKSILKKT NE YNIFVDS DPM MSDKTT MQKE HYKIF NFFKT VVSA YRNNVA KNN PFE |
-Macromolecule #4: Type IV secretion system apparatus protein CagX
Macromolecule | Name: Type IV secretion system apparatus protein CagX / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MKLRASVLIG ATILCLILSA CSNYAKKVVK QKNHVYTPVY NELIEKYSEI PLNDKLKDTP FMVQVKLPN YKDYLLDNKQ VVLTFKLVHH SKKITLIGDA NKILQYKNYF QANGARSDID F YLQPTLNQ KGVVMIASNY NDNPNSKEKP QTFDVLQGSQ PMLGANTKNL ...String: MKLRASVLIG ATILCLILSA CSNYAKKVVK QKNHVYTPVY NELIEKYSEI PLNDKLKDTP FMVQVKLPN YKDYLLDNKQ VVLTFKLVHH SKKITLIGDA NKILQYKNYF QANGARSDID F YLQPTLNQ KGVVMIASNY NDNPNSKEKP QTFDVLQGSQ PMLGANTKNL HGYDVSGANN KQ VINEVAR EKAQLEKINQ YYKTLLQDKE QEYTTRKNNQ REILETLSNR AGYQMRQNVI SSE IFKNGN LNMQAKEEEV REKLQEEREN EYLRNQIRSL LSGK |
-Macromolecule #5: Cag pathogenicity island protein (Cag7)
Macromolecule | Name: Cag pathogenicity island protein (Cag7) / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQL EKDETISYIT TGFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT R DYQEFLKT KKLIVDAPDP KELEEQKKAL EKEKEAKEQA QKAQKDKREK ...String: MGQAFFKKIV GCFCLGYLFL SSAIEAAALD IKNFNRGRVK VVNKKIAYLG DEKPITIWTS LDNVTVIQL EKDETISYIT TGFNKGWSIV PNSNHIFIQP KSVKSNLMFE KEAVNFALMT R DYQEFLKT KKLIVDAPDP KELEEQKKAL EKEKEAKEQA QKAQKDKREK RKEERAKNRA NL ENLTNAM SNPQNLSNNK NLSEFIKQQR ENELDQMERL EDMQEQAQAN ALKQIEELNK KQA EETIKQ RAKDKINIKT DKPQKSPEDN SIELSPSDSA WRTNLVVRTN KALYQFILRI AQKD NFASA YLTVKLEYPQ RHEVSSVIEE ELKKREEAKR QKELIKQENL NTTAYINRVM MASNE QIIN KEKIREEKQK IILDQAKALE TQYVHNALKR NPVPRNYNYY QAPEKRSKHI MPSEIF DDG TFTYFGFKNI TLQPAIFVVQ PDGKLSMTDA AIDPNMTNSG LRWYRVNEIA EKFKLIK DK ALVTVINKGY GKNPLTKNYN IKNYGELERV IKKLPLVRDK |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.4 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: NITROGEN |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |