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Yorodumi- EMDB-13083: L. pneumophila Type IV Coupling Complex (T4CC) with density for D... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13083 | |||||||||
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Title | L. pneumophila Type IV Coupling Complex (T4CC) with density for DotY N-terminal and middle domains | |||||||||
Map data | L. pneumophila Type IV Coupling Complex (T4CC) with DotY density | |||||||||
Sample |
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Keywords | Type IV Coupling Complex / T4CC / Type IV Secretion System / T4SS / Membrane protein complex / Membrane complex / DotY / DotZ / DotL / DotM / DotN / IcmSW / Legionella / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) / Legionella pneumophila subsp. pneumophila str. Philadelphia 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 Å | |||||||||
Authors | Mace K / Meir A | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Mol Microbiol / Year: 2022 Title: Proteins DotY and DotZ modulate the dynamics and localization of the type IVB coupling complex of Legionella pneumophila. Authors: Kevin Macé / Amit Meir / Natalya Lukoyanova / Luying Liu / David Chetrit / Manuela K Hospenthal / Craig R Roy / Gabriel Waksman / Abstract: Legionella pneumophila is an opportunistic pathogen infecting alveolar macrophages and protozoa species. Legionella utilizes a Type IV Secretion System (T4SS) to translocate over 300 effector ...Legionella pneumophila is an opportunistic pathogen infecting alveolar macrophages and protozoa species. Legionella utilizes a Type IV Secretion System (T4SS) to translocate over 300 effector proteins into its host cell. In a recent study, we have isolated and solved the cryo-EM structure of the Type IV Coupling Complex (T4CC), a large cytoplasmic determinant associated with the inner membrane that recruits effector proteins for delivery to the T4SS for translocation. The T4CC is composed of a DotLMNYZ hetero-pentameric core from which the flexible IcmSW module flexibly protrudes. The DotY and DotZ proteins were newly reported members of this complex and their role remained elusive. In this study, we observed the effect of deleting DotY and DotZ on T4CC stability and localization. Furthermore, we found these two proteins are co-dependent, whereby the deletion of DotY resulted in DotZ absence from the coupling complex, and vice versa. Additional cryo-EM data analysis revealed the dynamic movement of the IcmSW module is modified by the DotY/Z proteins. We therefore determined the likely function of DotY and DotZ and revealed their importance on T4CC function. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13083.map.gz | 95 MB | EMDB map data format | |
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Header (meta data) | emd-13083-v30.xml emd-13083.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
Images | emd_13083.png | 68.9 KB | ||
Filedesc metadata | emd-13083.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13083 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13083 | HTTPS FTP |
-Validation report
Summary document | emd_13083_validation.pdf.gz | 536.8 KB | Display | EMDB validaton report |
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Full document | emd_13083_full_validation.pdf.gz | 536.3 KB | Display | |
Data in XML | emd_13083_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_13083_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13083 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13083 | HTTPS FTP |
-Related structure data
Related structure data | 7ovbMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13083.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | L. pneumophila Type IV Coupling Complex (T4CC) with DotY density | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : T4CC pentameric core complex with DotY middle domain
Entire | Name: T4CC pentameric core complex with DotY middle domain |
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Components |
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-Supramolecule #1: T4CC pentameric core complex with DotY middle domain
Supramolecule | Name: T4CC pentameric core complex with DotY middle domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) |
-Macromolecule #1: IcmO (DotL)
Macromolecule | Name: IcmO (DotL) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 |
Molecular weight | Theoretical: 87.600992 KDa |
Recombinant expression | Organism: Legionella pneumophila (bacteria) |
Sequence | String: MMRGIDSRHE LDPTLLLRDT RTFTQRLADF FADPTNISIV LISLAAVSYY FSEAATFLLI MGGIFFLYSY TRKQKLPFRL PQISRAKDY NDLKPGINKP NIARGITFFG NDRKTGEELW FANDDMRTHA LIFGSTGSGK TETLVSLSYN ALVQGSGFIY V DGKGDNSL ...String: MMRGIDSRHE LDPTLLLRDT RTFTQRLADF FADPTNISIV LISLAAVSYY FSEAATFLLI MGGIFFLYSY TRKQKLPFRL PQISRAKDY NDLKPGINKP NIARGITFFG NDRKTGEELW FANDDMRTHA LIFGSTGSGK TETLVSLSYN ALVQGSGFIY V DGKGDNSL YAKVFSMVRS MGREDDLLLI NFMTGARDIV GPQEKRLSNT LNPFCQGSSS MLTQLVVSLM GSSGQSSDGD MW KGRAIAF VEALMRLLVY MRDEGAILLD ANTIRNYFDL QRLESIVIDK VFPRDDQESV NIETIPKLVT DPLRNYLNTL PGY NKEKKG KQVSQVLEQH GFITMQLVRS FSSLADTYGH IIRTNLAEVD FKDVVLNRRI LVVLLPALEK SPDELSNLGK IIVS SLKAM MAAGLGEEVE GDYRDVILRK PTNAPTPYMC ILDEYGYYAV QGFAVVPAQA RSLGFSAIFA GQDLPAFQKA SKEEA ASIG ANTNIKICMK LEDPTETWDF FTKTAGEAYV TKVDSFQTKE TSIANSYMDT KSSSFEKRAR VDLLDLKEQT EGEAHI FFK SKIVRARMFY ANPKPVKQLK INQFLKVEPP PDDYLMKLQK QLASFQSILE SGDLSINKAV ENEEITLISK ALKESTI VE PIERGVAALI AFHGQNEPEP VEDIVEEEVE GALTIFSKLR IDPNAPPILV ADKEVFSEPL LPINETRNQM ITIERLAG A KDKYAGTVAN ELIKDFQIAT SYPPEERDVI DVQELTGIIR DLSAKISAER EKANKKAAEE LT UniProtKB: Type 4 coupling protein DotL |
-Macromolecule #2: IcmP (DotM)
Macromolecule | Name: IcmP (DotM) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 |
Molecular weight | Theoretical: 43.858879 KDa |
Recombinant expression | Organism: Legionella pneumophila (bacteria) |
Sequence | String: MYIEMAQQQQ QSGSDNSMAP VWIVILLFIT AYFVWALAHQ YIVSFVFTIN IWQARLVNLF LNNQLLANQI YLMQTLDPNT VNWDQMVTV MRAVGDYMRY PVICILVVLA FVLYNSNVTL KYRKTYDMKS LRAQEQFNWP AIMPIVKEDL VSQDVNKGPW A MALTPMEF ...String: MYIEMAQQQQ QSGSDNSMAP VWIVILLFIT AYFVWALAHQ YIVSFVFTIN IWQARLVNLF LNNQLLANQI YLMQTLDPNT VNWDQMVTV MRAVGDYMRY PVICILVVLA FVLYNSNVTL KYRKTYDMKS LRAQEQFNWP AIMPIVKEDL VSQDVNKGPW A MALTPMEF ARKYNLLRKD DALLDNPVPG EEMTAGIRRG DAKRVFTMQL GPYWDGFERC SPQAYALSAV FMARMNRDRD AA NNILKVL DKTFVDGKPD FSVARPVMKK YQNSELVQEV VAKHAYVLTV IASLLEAARE DGVVPSSEFL WLKPVDRRLW YML NCVGRQ TPYSEVAGPF AHWKAEKEMG RRSLVPMIDE AIRALEIAVK EVRLTPRQME ELEP UniProtKB: Type 4 apparatus protein DotM |
-Macromolecule #3: IcmJ (DotN)
Macromolecule | Name: IcmJ (DotN) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 |
Molecular weight | Theoretical: 23.762971 KDa |
Recombinant expression | Organism: Legionella pneumophila (bacteria) |
Sequence | String: MADNQQRCEL KLIASPGSWR LYSARKIDER FKSYEQKIFQ RDRYTCQFCG FQARLYQDIV NLDGDYTNNR LSNLVTACCF CAQCFFVES VGVGGYGGGT LIYLPELTQA ELNSLCHVLF CAITNDTGYK SSAQNIYRSF KFRSQIVEEK FGEGTSDPAI F GQLMIDSG ...String: MADNQQRCEL KLIASPGSWR LYSARKIDER FKSYEQKIFQ RDRYTCQFCG FQARLYQDIV NLDGDYTNNR LSNLVTACCF CAQCFFVES VGVGGYGGGT LIYLPELTQA ELNSLCHVLF CAITNDTGYK SSAQNIYRSF KFRSQIVEEK FGEGTSDPAI F GQLMIDSG VNSEEIREKL FKNIRLLPSR AKFRKQIEKW AASALEEIAD UniProtKB: Type 4 apparatus protein DotN |
-Macromolecule #4: DotZ
Macromolecule | Name: DotZ / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 |
Molecular weight | Theoretical: 33.887512 KDa |
Recombinant expression | Organism: Legionella pneumophila (bacteria) |
Sequence | String: MDEIKKDDEL SQWLSTYGTI TAERILGRYN ISLPQDEILE AINIPSSFYR HLLQIPLKNV LNGIVIQQAS DYHVYAQKLL IDYLLSGES SKEPDSQGAG TRESLEDERQ RLVQLGDEFH KLELEQDNLI ASSQASLMKI SIDWNTKLET TLSKLNSLYK N TNSKIKKN ...String: MDEIKKDDEL SQWLSTYGTI TAERILGRYN ISLPQDEILE AINIPSSFYR HLLQIPLKNV LNGIVIQQAS DYHVYAQKLL IDYLLSGES SKEPDSQGAG TRESLEDERQ RLVQLGDEFH KLELEQDNLI ASSQASLMKI SIDWNTKLET TLSKLNSLYK N TNSKIKKN AIRKALIKAF IHCDLVKDQS QKNKYQLIDK LNQTLAVSVG AELKESILTN LSELFQILEA LNTKLDEFTD RT NHLSQQA KSFRTQFYEV ILRIIELIKL LPEYKIDPAQ DAINREPLYF DRTIGER UniProtKB: Type 4 apparatus protein DotZ |
-Macromolecule #5: DotY
Macromolecule | Name: DotY / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 |
Molecular weight | Theoretical: 25.550957 KDa |
Recombinant expression | Organism: Legionella pneumophila (bacteria) |
Sequence | String: MPKYTLPTRD ALLKAMQVGE TSIEAAEYMA TRFEQILTKA KLLPECNDML EKIKEYAQFV KFKLLSSAQV WSGQERPTSD YQNTQENKA EFLASHLEGL PSGLKLEVAI GDDAKILRGF SSNGKMVEGD QLKTMDGLLE GWLAKNSLAI SGGAVVKIDN T GNQTKVDP ...String: MPKYTLPTRD ALLKAMQVGE TSIEAAEYMA TRFEQILTKA KLLPECNDML EKIKEYAQFV KFKLLSSAQV WSGQERPTSD YQNTQENKA EFLASHLEGL PSGLKLEVAI GDDAKILRGF SSNGKMVEGD QLKTMDGLLE GWLAKNSLAI SGGAVVKIDN T GNQTKVDP QEIRQLINDS EKGVAKYFAD KGVGMEVAQR TYQEPKALET KREEIRQEIE SGAEAPTTQS IR UniProtKB: Type 4 apparatus protein DotY |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183397 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |