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- EMDB-12519: Periplasmic assembly of the intact ESX-5 inner membrane complex, ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12519
TitlePeriplasmic assembly of the intact ESX-5 inner membrane complex, C3 symmetry
Map data-50 Bfactor sharpening of 3D refinement map.
Sample
  • Complex: Periplasmic assembly of the intact ESX-5 inner membrane complex, C3 symmetry
    • Protein or peptide: ESX-5 secretion system protein EccB5
    • Protein or peptide: ESX-5 secretion system protein MycP5
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 H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsBunduc CM / Fahrenkamp D / Wald J / Ummels R / Bitter W / Houben ENG / Marlovits TC
Funding support Germany, Netherlands, European Union, 4 items
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, 2021-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateJun 2, 2021-
Current statusJun 2, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12519.png

Downloads & links

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Map

FileDownload / File: emd_12519.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation-50 Bfactor sharpening of 3D refinement map.
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.034890004 - 0.081768736
Average (Standard dev.)0.0003054551 (±0.0028036502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 275.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z275.000275.000275.000
α/β/γ90.00090.00090.000
start NX/NY/NZ7297100
NX/NY/NZ181127145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0350.0820.000

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Supplemental data

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Mask #1

Fileemd_12519_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D refinement map.

Fileemd_12519_additional_1.map
Annotation3D refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half1 of 3D refinement map.

Fileemd_12519_half_map_1.map
AnnotationHalf1 of 3D refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half2 of 3D refinement map.

Fileemd_12519_half_map_2.map
AnnotationHalf2 of 3D refinement map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Periplasmic assembly of the intact ESX-5 inner membrane complex, ...

EntireName: Periplasmic assembly of the intact ESX-5 inner membrane complex, C3 symmetry
Components
  • Complex: Periplasmic assembly of the intact ESX-5 inner membrane complex, C3 symmetry
    • Protein or peptide: ESX-5 secretion system protein EccB5
    • Protein or peptide: ESX-5 secretion system protein MycP5

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Supramolecule #1: Periplasmic assembly of the intact ESX-5 inner membrane complex, ...

SupramoleculeName: Periplasmic assembly of the intact ESX-5 inner membrane complex, C3 symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)

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Macromolecule #1: ESX-5 secretion system protein EccB5

MacromoleculeName: ESX-5 secretion system protein EccB5 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MAEESRGQRG SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEIEPGR RQTLAVVASV SAALVICLG ALLWSFISPS GQLNESPIIA DRDSGALYVR VGDRLYPALN LASARLITGR P DNPHLVRS SQIATMPRGP LVGIPGAPSS FSPKSPPASS WLVCDTVATS ...String:
MAEESRGQRG SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEIEPGR RQTLAVVASV SAALVICLG ALLWSFISPS GQLNESPIIA DRDSGALYVR VGDRLYPALN LASARLITGR P DNPHLVRS SQIATMPRGP LVGIPGAPSS FSPKSPPASS WLVCDTVATS SSIGSLQGVT VT VIDGTPD LTGHRQILSG SDAVVLRYGG DAWVIREGRR SRIEPTNRAV LLPLGLTPEQ VSQ ARPMSR ALFDALPVGP ELLVPEVPNA GGPATFPGAP GPIGTVIVTP QISGPQQYSL VLGD GVQTL PPLVAQILQN AGSAGNTKPL TVEPSTLAKM PVVNRLDLSA YPDNPLEVVD IREHP STCW WWERTAGENR ARVRVVSGPT IPVAATEMNK VVSLVKADTS GRQADQVYFG PDHANF VAV TGNNPGAQTS ESLWWVTDAG ARFGVEDSKE ARDALGLTLT PSLAPWVALR LLPQGPT LS RADALVEHDT LPMDMTPAEL VVPK

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Macromolecule #2: ESX-5 secretion system protein MycP5

MacromoleculeName: ESX-5 secretion system protein MycP5 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MQRFGTGSSR SWCGRAGTAT IAAVLLASGA LTGLPPAYAI SPPTIDPGAL PPDGPPGPLA PMKQNAYCT EVGVLPGTDF QLQPKYMEML NLNEAWQFGR GDGVKVAVID TGVTPHPRLP R LIPGGDYV MAGGDGLSDC DAHGTLVASM IAAVPANGAV PLPSVPRRPV ...String:
MQRFGTGSSR SWCGRAGTAT IAAVLLASGA LTGLPPAYAI SPPTIDPGAL PPDGPPGPLA PMKQNAYCT EVGVLPGTDF QLQPKYMEML NLNEAWQFGR GDGVKVAVID TGVTPHPRLP R LIPGGDYV MAGGDGLSDC DAHGTLVASM IAAVPANGAV PLPSVPRRPV TIPTTETPPP PQ TVTLSPV PPQTVTVIPA PPPEEGVPPG APVPGPEPPP APGPQPPAVD RGGGTVTVPS YSG GRKIAP IDNPRNPHPS APSPALGPPP DAFSGIAPGV EIISIRQSSQ AFGLKDPYTG DEDP QTAQK IDNVETMARA IVHAANMGAS VINISDVMCM SARNVIDQRA LGAAVHYAAV DKDAV IVAA AGDGSKKDCK QNPIFDPLQP DDPRAWNAVT TVVTPSWFHD YVLTVGAVDA NGQPLS KMS IAGPWVSISA PGTDVVGLSP RDDGLINAID GPDNSLLVPA GTSFSAAIVS GVAALVR AK FPELSAYQII NRLIHTARPP ARGVDNQVGY GVVDPVAALT WDVPKGPAEP PKQLSAPL V VPQPPAPRDM VPIWVAAGGL AGALLIGGAV FGTATLMRRS RKQQ

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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-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 59.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER / Details: Rotationally averaged 3D structure.
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154929
FSC plot (resolution estimation)

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