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- PDB-7nps: Structure of the periplasmic assembly from the ESX-5 inner membra... -

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Basic information

Entry
Database: PDB / ID: 7nps
TitleStructure of the periplasmic assembly from the ESX-5 inner membrane complex, C1 model
Components
  • ESX-5 secretion system ATPase EccB5
  • Mycosin-5
KeywordsMEMBRANE PROTEIN / T7SS / mycobacteria / protein transport / secretion / type VII secretion system / membrane
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / peptidoglycan-based cell wall / protein processing / hydrolase activity / serine-type endopeptidase activity / ATP binding / membrane / plasma membrane
Similarity search - Function
Type VII secretion system peptidase S8A, mycosin / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system ESX-1, transport TM domain B / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related ...Type VII secretion system peptidase S8A, mycosin / Type VII secretion system EccB, repeat 1 domain / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system ESX-1, transport TM domain B / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain
Similarity search - Domain/homology
Mycosin-5 / ESX-5 secretion system ATPase EccB5
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsFahrenkamp, D. / Bunduc, C.M. / Wald, J. / Ummels, R. / Bitter, W. / Houben, E.N.G. / Marlovits, T.C.
Funding support Germany, Netherlands, European Union, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 152/774-1 FUGG Germany
Netherlands Organisation for Scientific Research (NWO)864.12.006 Netherlands
H2020 Marie Curie Actions of the European Commission101030373European Union
German Research Foundation (DFG)FA1518/2-1 Germany
CitationJournal: Nature / Year: 2021
Title: Structure and dynamics of a mycobacterial type VII secretion system.
Authors: Catalin M Bunduc / Dirk Fahrenkamp / Jiri Wald / Roy Ummels / Wilbert Bitter / Edith N G Houben / Thomas C Marlovits /
Abstract: Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year. Specialized protein transport systems-known as ...Mycobacterium tuberculosis is the cause of one of the most important infectious diseases in humans, which leads to 1.4 million deaths every year. Specialized protein transport systems-known as type VII secretion systems (T7SSs)-are central to the virulence of this pathogen, and are also crucial for nutrient and metabolite transport across the mycobacterial cell envelope. Here we present the structure of an intact T7SS inner-membrane complex of M. tuberculosis. We show how the 2.32-MDa ESX-5 assembly, which contains 165 transmembrane helices, is restructured and stabilized as a trimer of dimers by the MycP protease. A trimer of MycP caps a central periplasmic dome-like chamber that is formed by three EccB dimers, with the proteolytic sites of MycP facing towards the cavity. This chamber suggests a central secretion and processing conduit. Complexes without MycP show disruption of the EccB periplasmic assembly and increased flexibility, which highlights the importance of MycP for complex integrity. Beneath the EccB-MycP chamber, dimers of the EccC ATPase assemble into three bundles of four transmembrane helices each, which together seal the potential central secretion channel. Individual cytoplasmic EccC domains adopt two distinctive conformations that probably reflect different secretion states. Our work suggests a previously undescribed mechanism of protein transport and provides a structural scaffold to aid in the development of drugs against this major human pathogen.
History
DepositionFeb 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name

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Structure visualization

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Assembly

Deposited unit
B1: ESX-5 secretion system ATPase EccB5
B2: ESX-5 secretion system ATPase EccB5
B3: ESX-5 secretion system ATPase EccB5
B4: ESX-5 secretion system ATPase EccB5
B5: ESX-5 secretion system ATPase EccB5
B6: ESX-5 secretion system ATPase EccB5
P1: Mycosin-5
P2: Mycosin-5
P3: Mycosin-5


Theoretical massNumber of molelcules
Total (without water)502,8439
Polymers502,8439
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area28710 Å2
ΔGint-132 kcal/mol
Surface area167830 Å2
MethodPISA

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Components

#1: Protein
ESX-5 secretion system ATPase EccB5 / ESX conserved component B5 / Type VII secretion system protein EccB5 / T7SS protein EccB5


Mass: 53769.988 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: eccB5, Rv1782
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: P9WNQ9, Hydrolases; Acting on acid anhydrides
#2: Protein Mycosin-5 / MycP5 protease


Mass: 60074.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: mycP5, Rv1796, LH57_09820
Production host: Mycolicibacterium smegmatis MC2 155 (bacteria)
References: UniProt: O53945, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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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: Periplasmic assembly of the ESX-5 inner membrane complex
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Mycolicibacterium smegmatis MC2 155 (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 59.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.18.2_3874refinement
PHENIX1.18.2_3874refinement
ISOLDE1.1.0model building
UCSF ChimeraX1.1/v9model building
EM software
IDNameVersionCategory
7ISOLDE1.0.1model fitting
9ISOLDE1.0.1model refinement
10PHENIX1.18model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 154929 / Symmetry type: POINT

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