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- EMDB-12518: Structure of the periplasmic assembly from the ESX-5 inner membra... -

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Basic information

Entry
Database: EMDB / ID: EMD-12518
TitleStructure of the periplasmic assembly from the ESX-5 inner membrane complex, C1 symmetry
Map data-50 Bfactor sharpening of 3D refinement map.
Sample
  • Complex: Periplasmic assembly of the ESX-5 inner membrane complex
    • Protein or peptide: ESX-5 secretion system ATPase EccB5
    • Protein or peptide: Mycosin-5
KeywordsT7SS / mycobacteria / protein transport / secretion / type VII secretion system / membrane / MEMBRANE PROTEIN
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 / plasma membrane
Similarity search - Function
Type VII secretion system peptidase S8A, mycosin / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. ...Type VII secretion system peptidase S8A, mycosin / Type VII secretion system EccB / Type VII secretion system EccB, repeat 3 domain / Type VII secretion system EccB, repeat 1 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 / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / 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) / Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing 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
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nps
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12518.png

Downloads & links

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Map

FileDownload / File: emd_12518.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.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å		1.1 Å/pix.
x 250 pix.
= 275. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.035574585 - 0.0759777
Average (Standard dev.)0.00030927212 (±0.0026691244)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0360.0760.000

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Supplemental data

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Mask #1

Fileemd_12518_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D refinement map.

Fileemd_12518_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_12518_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_12518_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 ESX-5 inner membrane complex

EntireName: Periplasmic assembly of the ESX-5 inner membrane complex
Components
  • Complex: Periplasmic assembly of the ESX-5 inner membrane complex
    • Protein or peptide: ESX-5 secretion system ATPase EccB5
    • Protein or peptide: Mycosin-5

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

SupramoleculeName: Periplasmic assembly of the ESX-5 inner membrane complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

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Macromolecule #1: ESX-5 secretion system ATPase EccB5

MacromoleculeName: ESX-5 secretion system ATPase EccB5 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: Hydrolases; Acting on acid anhydrides
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv
Molecular weightTheoretical: 53.769988 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MAEESRGQRG SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEIEPGR RQTLAVVASV SAALVICLGA LLWSFISPSG QLNESPIIA DRDSGALYVR VGDRLYPALN LASARLITGR PDNPHLVRSS QIATMPRGPL VGIPGAPSSF SPKSPPASSW L VCDTVATS ...String:
MAEESRGQRG SGYGLGLSTR TQVTGYQFLA RRTAMALTRW RVRMEIEPGR RQTLAVVASV SAALVICLGA LLWSFISPSG QLNESPIIA DRDSGALYVR VGDRLYPALN LASARLITGR PDNPHLVRSS QIATMPRGPL VGIPGAPSSF SPKSPPASSW L VCDTVATS SSIGSLQGVT VTVIDGTPDL TGHRQILSGS DAVVLRYGGD AWVIREGRRS RIEPTNRAVL LPLGLTPEQV SQ ARPMSRA LFDALPVGPE LLVPEVPNAG GPATFPGAPG PIGTVIVTPQ ISGPQQYSLV LGDGVQTLPP LVAQILQNAG SAG NTKPLT VEPSTLAKMP VVNRLDLSAY PDNPLEVVDI REHPSTCWWW ERTAGENRAR VRVVSGPTIP VAATEMNKVV SLVK ADTSG RQADQVYFGP DHANFVAVTG NNPGAQTSES LWWVTDAGAR FGVEDSKEAR DALGLTLTPS LAPWVALRLL PQGPT LSRA DALVEHDTLP MDMTPAELVV PK

UniProtKB: ESX-5 secretion system ATPase EccB5

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Macromolecule #2: Mycosin-5

MacromoleculeName: Mycosin-5 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Source (natural)Organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv
Molecular weightTheoretical: 60.074211 KDa
Recombinant expressionOrganism: Mycolicibacterium smegmatis MC2 155 (bacteria)
SequenceString: MQRFGTGSSR SWCGRAGTAT IAAVLLASGA LTGLPPAYAI SPPTIDPGAL PPDGPPGPLA PMKQNAYCTE VGVLPGTDFQ LQPKYMEML NLNEAWQFGR GDGVKVAVID TGVTPHPRLP RLIPGGDYVM AGGDGLSDCD AHGTLVASMI AAVPANGAVP L PSVPRRPV ...String:
MQRFGTGSSR SWCGRAGTAT IAAVLLASGA LTGLPPAYAI SPPTIDPGAL PPDGPPGPLA PMKQNAYCTE VGVLPGTDFQ LQPKYMEML NLNEAWQFGR GDGVKVAVID TGVTPHPRLP RLIPGGDYVM AGGDGLSDCD AHGTLVASMI AAVPANGAVP L PSVPRRPV TIPTTETPPP PQTVTLSPVP PQTVTVIPAP PPEEGVPPGA PVPGPEPPPA PGPQPPAVDR GGGTVTVPSY SG GRKIAPI DNPRNPHPSA PSPALGPPPD AFSGIAPGVE IISIRQSSQA FGLKDPYTGD EDPQTAQKID NVETMARAIV HAA NMGASV INISDVMCMS ARNVIDQRAL GAAVHYAAVD KDAVIVAAAG DGSKKDCKQN PIFDPLQPDD PRAWNAVTTV VTPS WFHDY VLTVGAVDAN GQPLSKMSIA GPWVSISAPG TDVVGLSPRD DGLINAIDGP DNSLLVPAGT SFSAAIVSGV AALVR AKFP ELSAYQIINR LIHTARPPAR GVDNQVGYGV VDPVAALTWD VPKGPAEPPK QLSAPLVVPQ PPAPRDMVPI WVAAGG LAG ALLIGGAVFG TATLMRRSRK QQ

UniProtKB: Mycosin-5

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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154929
Initial angle assignmentType: OTHER / Details: Rotationally averaged 3D structure.
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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