[English] 日本語
Yorodumi
- PDB-7sgr: Structure of hemolysin A secretion system HlyB/D complex -

+
Open data


ID or keywords:

Loading...

-
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. / : / ATPase, type I secretion system, HlyB / Peptidase C39-like A / : / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing ...Secretion protein HlyD, conserved site / Type I secretion membrane fusion protein, HlyD family / HlyD family secretion proteins signature. / : / ATPase, type I secretion system, HlyB / Peptidase C39-like A / : / Peptidase family C39 domain profile. / Peptidase C39 family / Peptidase C39, bacteriocin processing / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more