+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25116 | |||||||||
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Title | Structure of hemolysin A secretion system HlyB/D complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | hydrolase / transport / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information type I protein secretion system complex / protein secretion by the type I secretion system / ATPase-coupled lipid transmembrane transporter activity / protein secretion / ABC-type transporter activity / peptidase activity / killing of cells of another organism / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli O6:H1 (bacteria) / Escherichia coli CFT073 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Zhao H / Chen J | |||||||||
Funding support | France, United States, 2 items
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Citation | Journal: Cell / Year: 2022 Title: The hemolysin A secretion system is a multi-engine pump containing three ABC transporters. Authors: Hongtu Zhao / James Lee / Jue Chen / Abstract: Type 1 secretion systems (T1SSs) are widespread in pathogenic Gram-negative bacteria, extruding protein substrates following synthesis of the entire polypeptide. The Escherichia coli hemolysin A ...Type 1 secretion systems (T1SSs) are widespread in pathogenic Gram-negative bacteria, extruding protein substrates following synthesis of the entire polypeptide. The Escherichia coli hemolysin A secretion system has long been considered a prototype in structural and mechanistic studies of T1SSs. Three membrane proteins-an inner membrane ABC transporter HlyB, an adaptor protein HlyD, and an outer membrane porin TolC-are required for secretion. However, the stoichiometry and structure of the complex are unknown. Here, cryo-electron microscopy (cryo-EM) structures determined in two conformations reveal that the inner membrane complex is a hetero-dodecameric assembly comprising three HlyB homodimers and six HlyD subunits. Functional studies indicate that oligomerization of HlyB and HlyD is essential for protein secretion and that polypeptides translocate through a canonical ABC transporter pathway in HlyB. Our data suggest that T1SSs entail three ABC transporters, one that functions as a protein channel and two that allosterically power the translocation process. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_25116.map.gz | 204.2 MB | EMDB map data format | |
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Header (meta data) | emd-25116-v30.xml emd-25116.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | emd_25116.png | 122.6 KB | ||
Filedesc metadata | emd-25116.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25116 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25116 | HTTPS FTP |
-Related structure data
Related structure data | 7sgrMC 8dckC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25116.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Membrane protein complex of HlyB and HlyD
Entire | Name: Membrane protein complex of HlyB and HlyD |
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Components |
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-Supramolecule #1: Membrane protein complex of HlyB and HlyD
Supramolecule | Name: Membrane protein complex of HlyB and HlyD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli O6:H1 (bacteria) |
Molecular weight | Theoretical: 810 KDa |
-Macromolecule #1: Alpha-hemolysin translocation ATP-binding protein HlyB
Macromolecule | Name: Alpha-hemolysin translocation ATP-binding protein HlyB type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli CFT073 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC |
Molecular weight | Theoretical: 79.621492 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDSCHKIDYG LYALEILAQY HNVSVNPEEI KHRFDTDGTG LGLTSWLLAA KSLELKVKQV KKTIDRLNFI SLPALVWRED GRHFILTKV SKEANRYLIF DLEQRNPRVL EQSEFEALYQ GHIILIASRS SVTGKLAKFD FTWFIPAIIK YRKIFIETLV V SVFLQLFA ...String: MDSCHKIDYG LYALEILAQY HNVSVNPEEI KHRFDTDGTG LGLTSWLLAA KSLELKVKQV KKTIDRLNFI SLPALVWRED GRHFILTKV SKEANRYLIF DLEQRNPRVL EQSEFEALYQ GHIILIASRS SVTGKLAKFD FTWFIPAIIK YRKIFIETLV V SVFLQLFA LITPLFFQVV MDKVLVHRGF STLNVITVAL SVVVVFEIIL SGLRTYIFAH STSRIDVELG AKLFRHLLAL PI SYFESRR VGDTVARVRE LDQIRNFLTG QALTSVLDLL FSFIFFAVMW YYSPKLTLVI LFSLPCYAAW SVFISPILRR RLD DKFSRN ADNQSFLVES VTAINTIKAM AVSPQMTNIW DKQLAGYVAA GFKVTVLATI GQQGIQLIQK TVMIINLWLG AHLV ISGDL SIGQLIAFNM LAGQIVAPVI RLAQIWQDFQ QVGISVTRLG DVLNSPTESY HGKLALPEIN GNITFRNIRF RYKPD SPVI LDNINLSIKQ GEVIGIVGRS GSGKSTLTKL IQRFYIPENG QVLIDGHDLA LADPNWLRRQ VGVVLQDNVL LNRSII DNI SLANPGMSVE KVIYAAKLAG AHDFISELRE GYNTIVGEQG AGLSGGQRQR IAIARALVNN PKILIFDEAT SALDYES EH IIMRNMHKIC KGRTVIIIAH RLSTVKNADR IIVMEKGKIV EQGKHKELLS EPESLYSYLY QLQSD UniProtKB: Alpha-hemolysin translocation ATP-binding protein HlyB |
-Macromolecule #2: Membrane fusion protein (MFP) family protein,Hemolysin secretion ...
Macromolecule | Name: Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli CFT073 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC |
Molecular weight | Theoretical: 40.748895 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKTWLMGFSE FLLRYKLVWS ETWKIRKQLD TPVREKDENE FLPAHLELIE TPVSRRPRLV AYFIMGFLVI AVILSVLGQV EIVATANGK LTLSGRSKEI KPIENSIVKE IIVKEGESVR KGDVLLKLTA LGAEADTLKT QSSLLQTRLE QTRYQILSRS I ELNKLPEL ...String: MKTWLMGFSE FLLRYKLVWS ETWKIRKQLD TPVREKDENE FLPAHLELIE TPVSRRPRLV AYFIMGFLVI AVILSVLGQV EIVATANGK LTLSGRSKEI KPIENSIVKE IIVKEGESVR KGDVLLKLTA LGAEADTLKT QSSLLQTRLE QTRYQILSRS I ELNKLPEL KLPDEPYFQN VSEEEVLRLT SLIKEQFSTW QNQKYQKELN LDKKRAERLT ILARINRYEN LSRVEKSRLD DF DDTLEVT ALVQNKDIGF INVGQNAIIK VEAFPYTRYG YLVGKVKNIN LDAIEDQKLG LVFNVIVSVE ENDLSTGNKH IPL SSGMAV TAEIKTGMRS VISYLLSPLE ESVTESLHER UniProtKB: Membrane fusion protein (MFP) family protein, Hemolysin secretion protein D, chromosomal |
-Macromolecule #3: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyl...
Macromolecule | Name: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate type: ligand / ID: 3 / Number of copies: 37 / Formula: 6OU |
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Molecular weight | Theoretical: 717.996 Da |
Chemical component information | ChemComp-6OU: |
-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: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136123 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |