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- PDB-7sgr: Structure of hemolysin A secretion system HlyB/D complex -

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Basic information

Entry
Database: PDB / ID: 7sgr
TitleStructure of hemolysin A secretion system HlyB/D complex
Components
  • Alpha-hemolysin translocation ATP-binding protein HlyB
  • Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal
KeywordsMEMBRANE PROTEIN / hydrolase / transport
Function / homology
Function and homology information


type I protein secretion system complex / protein secretion by the type I secretion system / ABC-type oligopeptide transporter activity / protein secretion / peptidase activity / killing of cells of another organism / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
Secretion protein HlyD, conserved site / Type I secretion membrane fusion protein, HlyD family / HlyD family secretion proteins signature. / HlyD family secretion protein / : / ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. ...Secretion protein HlyD, conserved site / Type I secretion membrane fusion protein, HlyD family / HlyD family secretion proteins signature. / HlyD family secretion protein / : / ATPase, type I secretion system, HlyB / Peptidase C39-like A / Peptidase C39 family / Peptidase C39, bacteriocin processing / Peptidase family C39 domain profile. / ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / Cysteine proteinases / Cathepsin B; Chain A / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Alpha-Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-6OU / Membrane fusion protein (MFP) family protein / Hemolysin secretion protein D, chromosomal / Alpha-hemolysin translocation ATP-binding protein HlyB
Similarity search - Component
Biological speciesEscherichia coli CFT073 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsZhao, H. / Chen, J.
Funding support France, United States, 2items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP) France
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: 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
DepositionOct 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
J: Alpha-hemolysin translocation ATP-binding protein HlyB
I: Alpha-hemolysin translocation ATP-binding protein HlyB
A: Alpha-hemolysin translocation ATP-binding protein HlyB
B: Alpha-hemolysin translocation ATP-binding protein HlyB
E: Alpha-hemolysin translocation ATP-binding protein HlyB
F: Alpha-hemolysin translocation ATP-binding protein HlyB
H: Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal
L: Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal
D: Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal
C: Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal
G: Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal
K: Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)748,78849
Polymers722,22212
Non-polymers26,56637
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area76490 Å2
ΔGint-540 kcal/mol
Surface area189220 Å2

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Components

#1: Protein
Alpha-hemolysin translocation ATP-binding protein HlyB


Mass: 79621.492 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: hlyB, c3573 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8FDZ8
#2: Protein
Membrane fusion protein (MFP) family protein,Hemolysin secretion protein D, chromosomal


Mass: 40748.895 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Strain: CFT073 / ATCC 700928 / UPEC / Gene: hlyD, c3574, hlyD / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2VCZ1, UniProt: P09986
#3: Chemical...
ChemComp-6OU / [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate


Mass: 717.996 Da / Num. of mol.: 37 / Source method: obtained synthetically / Formula: C39H76NO8P / Comment: phospholipid*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Membrane protein complex of HlyB and HlyD / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.81 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli O6:H1 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136123 / Symmetry type: POINT

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