+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13153 | |||||||||||||||
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Title | 2.43 A Mycobacterium marinum EspB. | |||||||||||||||
Map data | Local B-factor sharpened map from LocSpiral | |||||||||||||||
Sample |
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Keywords | Cryo-EM / EspB / ESX-1 / Preferential orientation / PROTEIN TRANSPORT | |||||||||||||||
Function / homology | ESX-1 secretion-associated protein EspB, PE domain / ESX-1 secreted protein B PE domain / extracellular region / ESX-1 secretion-associated protein EspB Function and homology information | |||||||||||||||
Biological species | Mycobacterium marinum (bacteria) / Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.43 Å | |||||||||||||||
Authors | Gijsbers A / Zhang Y | |||||||||||||||
Funding support | Netherlands, European Union, Mexico, 4 items
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Citation | Journal: Curr Res Struct Biol / Year: 2021 Title: Priming mycobacterial ESX-secreted protein B to form a channel-like structure. Authors: Abril Gijsbers / Vanesa Vinciauskaite / Axel Siroy / Ye Gao / Giancarlo Tria / Anjusha Mathew / Nuria Sánchez-Puig / Carmen López-Iglesias / Peter J Peters / Raimond B G Ravelli / Abstract: ESX-1 is a major virulence factor of , a secretion machinery directly involved in the survival of the microorganism from the immune system defence. It disrupts the phagosome membrane of the host cell ...ESX-1 is a major virulence factor of , a secretion machinery directly involved in the survival of the microorganism from the immune system defence. It disrupts the phagosome membrane of the host cell through a contact-dependent mechanism. Recently, the structure of the inner-membrane core complex of the homologous ESX-3 and ESX-5 was resolved; however, the elements involved in the secretion through the outer membrane or those acting on the host cell membrane are unknown. Protein substrates might form this missing element. Here, we describe the oligomerisation process of the ESX-1 substrate EspB, which occurs upon cleavage of its C-terminal region and is favoured by an acidic environment. Cryo-electron microscopy data shows that quaternary structure of EspB is conserved across slow growing species, but not in the fast growing . EspB assembles into a channel with dimensions and characteristics suitable for the transit of ESX-1 substrates, as shown by the presence of another EspB trapped within. Our results provide insight into the structure and assembly of EspB, and suggests a possible function as a structural element of ESX-1. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13153.map.gz | 9.3 MB | EMDB map data format | |
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Header (meta data) | emd-13153-v30.xml emd-13153.xml | 21.7 KB 21.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13153_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_13153.png | 210.4 KB | ||
Masks | emd_13153_msk_1.map | 64 MB | Mask map | |
Filedesc metadata | emd-13153.cif.gz | 6.4 KB | ||
Others | emd_13153_additional_1.map.gz emd_13153_half_map_1.map.gz emd_13153_half_map_2.map.gz | 6.8 MB 49.5 MB 49.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13153 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13153 | HTTPS FTP |
-Validation report
Summary document | emd_13153_validation.pdf.gz | 915.1 KB | Display | EMDB validaton report |
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Full document | emd_13153_full_validation.pdf.gz | 914.7 KB | Display | |
Data in XML | emd_13153_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_13153_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13153 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13153 | HTTPS FTP |
-Related structure data
Related structure data | 7p0zMC 7p13C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13153.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Local B-factor sharpened map from LocSpiral | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.834 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_13153_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Global b-factor sharpened map from Relion postprocess.
File | emd_13153_additional_1.map | ||||||||||||
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Annotation | Global b-factor sharpened map from Relion postprocess. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unmasked halfmap 1 from Refine3D
File | emd_13153_half_map_1.map | ||||||||||||
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Annotation | Unmasked halfmap 1 from Refine3D | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unmasked halfmap 2 from Refine3D
File | emd_13153_half_map_2.map | ||||||||||||
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Annotation | Unmasked halfmap 2 from Refine3D | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heptamer of EspB
Entire | Name: Heptamer of EspB |
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Components |
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-Supramolecule #1: Heptamer of EspB
Supramolecule | Name: Heptamer of EspB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium marinum (bacteria) / Strain: BAA-535 |
Molecular weight | Theoretical: 210 KDa |
-Macromolecule #1: ESX-1 secretion-associated protein EspB
Macromolecule | Name: ESX-1 secretion-associated protein EspB / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria) Strain: ATCC BAA-535 / M |
Molecular weight | Theoretical: 31.274275 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SMHSQPQTVT VDQQEILNRA DEVEAPMATP PTDVPQAPSG LTAANNAAEQ LAVSADNVRL YLQAGERERQ RLATSLRNAA AAYGEVEDE SATALDNDGN GEVDAQSAGG AGAGQTESLE ETPKVAAAGE SDFTDLKTAA TKLESGDQGT SMVNFADGWN N FNLSLQRD ...String: SMHSQPQTVT VDQQEILNRA DEVEAPMATP PTDVPQAPSG LTAANNAAEQ LAVSADNVRL YLQAGERERQ RLATSLRNAA AAYGEVEDE SATALDNDGN GEVDAQSAGG AGAGQTESLE ETPKVAAAGE SDFTDLKTAA TKLESGDQGT SMVNFADGWN N FNLSLQRD IKRFRIFENW EGDAATACEA SMDQQKEWIL HMAKLSASLA KQANFMAQLQ LWARRGHPTL ADIVELERLA KD PDYQEQA IKLYAEYQET SEKVLSEYNT KADLEPVNPP KPPAAIKIDP P UniProtKB: ESX-1 secretion-associated protein EspB |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8.7 mg/mL | |||||||||
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Buffer | pH: 5.5 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | TFS KRIOS |
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Temperature | Min: 90.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Details | Basic direct alignments were done as well as astigmatism and coma alignment using AutoCTF |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2421 / Average exposure time: 1.8 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.25 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |