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- EMDB-13083: L. pneumophila Type IV Coupling Complex (T4CC) with density for D... -

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Basic information

Entry
Database: EMDB / ID: EMD-13083
TitleL. pneumophila Type IV Coupling Complex (T4CC) with density for DotY N-terminal and middle domains
Map dataL. pneumophila Type IV Coupling Complex (T4CC) with DotY density
Sample
  • Complex: T4CC pentameric core complex with DotY middle domain
    • Protein or peptide: IcmO (DotL)
    • Protein or peptide: IcmP (DotM)
    • Protein or peptide: IcmJ (DotN)
    • Protein or peptide: DotZ
    • Protein or peptide: DotY
  • Ligand: ZINC ION
Function / homology
Function and homology information


protein transport / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
TraD/TraG, TraM recognition site / TraM recognition site of TraD and TraG / HNH nucleases / HNH nuclease / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Type 4 apparatus protein DotZ / Type 4 apparatus protein DotN / Type 4 coupling protein DotL / Type 4 apparatus protein DotM / Type 4 apparatus protein DotY
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) / Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsMace K / Meir A / Lukoyanova N / Waksman G
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)321630 United Kingdom
Wellcome Trust098302/217089 United Kingdom
CitationJournal: 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
DepositionJun 14, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateFeb 23, 2022-
Current statusFeb 23, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ovb
  • Surface level: 8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13083.png

Downloads & links

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Map

FileDownload / File: emd_13083.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationL. pneumophila Type IV Coupling Complex (T4CC) with DotY density
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 8.0 / Movie #1: 8
Minimum - Maximum-21.045477 - 38.62444
Average (Standard dev.)-3.3443422e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 315.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z315.000315.000315.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-21.04538.624-0.000

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Supplemental data

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Sample components

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Entire : T4CC pentameric core complex with DotY middle domain

EntireName: T4CC pentameric core complex with DotY middle domain
Components
  • Complex: T4CC pentameric core complex with DotY middle domain
    • Protein or peptide: IcmO (DotL)
    • Protein or peptide: IcmP (DotM)
    • Protein or peptide: IcmJ (DotN)
    • Protein or peptide: DotZ
    • Protein or peptide: DotY
  • Ligand: ZINC ION

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Supramolecule #1: T4CC pentameric core complex with DotY middle domain

SupramoleculeName: T4CC pentameric core complex with DotY middle domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)

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Macromolecule #1: IcmO (DotL)

MacromoleculeName: IcmO (DotL) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Molecular weightTheoretical: 87.600992 KDa
Recombinant expressionOrganism: Legionella pneumophila (bacteria)
SequenceString: 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

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Macromolecule #2: IcmP (DotM)

MacromoleculeName: IcmP (DotM) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Molecular weightTheoretical: 43.858879 KDa
Recombinant expressionOrganism: Legionella pneumophila (bacteria)
SequenceString: 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

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Macromolecule #3: IcmJ (DotN)

MacromoleculeName: IcmJ (DotN) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Molecular weightTheoretical: 23.762971 KDa
Recombinant expressionOrganism: Legionella pneumophila (bacteria)
SequenceString: 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

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Macromolecule #4: DotZ

MacromoleculeName: DotZ / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Molecular weightTheoretical: 33.887512 KDa
Recombinant expressionOrganism: Legionella pneumophila (bacteria)
SequenceString: 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

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Macromolecule #5: DotY

MacromoleculeName: DotY / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1
Molecular weightTheoretical: 25.550957 KDa
Recombinant expressionOrganism: Legionella pneumophila (bacteria)
SequenceString: 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

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
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: OTHER / Imaging mode: OTHER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

10350

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 183397

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