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Yorodumi- EMDB-10658: CryoEM structure of the ring-shaped virulence factor EspB from My... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10658 | |||||||||
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Title | CryoEM structure of the ring-shaped virulence factor EspB from Mycobacterium tuberculosis | |||||||||
Map data | Sharped map | |||||||||
Sample |
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Keywords | M. tuberculosis / ESX-1 / Type VII secretion system / EspB / Rv3881c / EsxA / CFP10 / ESAT-6 / TRANSPORT PROTEIN | |||||||||
Function / homology | ESX-1 secretion-associated protein EspB, PE domain / ESX-1 secreted protein B PE domain / protein secretion by the type VII secretion system / PPE superfamily / biological process involved in interaction with host / extracellular region / identical protein binding / ESX-1 secretion-associated protein EspB Function and homology information | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) / Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.37 Å | |||||||||
Authors | Piton J / Pojer F | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: J Struct Biol X / Year: 2020 Title: High resolution CryoEM structure of the ring-shaped virulence factor EspB from . Authors: Jérémie Piton / Florence Pojer / Soichi Wakatsuki / Cornelius Gati / Stewart T Cole / Abstract: The EspB protein of is a 60 kDa virulence factor, implicated in conjugation and exported by the ESX-1 system of which it may also be a component. Previous attempts to obtain high-resolution maps of ...The EspB protein of is a 60 kDa virulence factor, implicated in conjugation and exported by the ESX-1 system of which it may also be a component. Previous attempts to obtain high-resolution maps of EspB by cryo-electron microscopic examination of single particles have been thwarted by severe orientation bias of the particles. This was overcome by using detergent as a surfactant thereby allowing reconstruction of the EspB structure at 3.37 Å resolution. The final structure revealed the N-terminal domain of EspB to be organized as a cylindrical heptamer with dimensions of 90 Å x 90 Å and a central channel of 45 Å diameter whereas the C-terminal domain was unstructured. New atomic insight was obtained into the helical packing required for protomer interactions and the overall electrostatic potential. The external surface is electronegatively charged while the channel is lined with electropositive patches. EspB thus has many features of a pore-like transport protein that might allow the passage of an ESX-1 substrate such as the 35 Å diameter EsxA-EsxB heterodimer or B-form DNA consistent with its proposed role in DNA uptake. | |||||||||
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_10658.map.gz | 230.2 MB | EMDB map data format | |
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Header (meta data) | emd-10658-v30.xml emd-10658.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
Images | emd_10658.png | 58 KB | ||
Masks | emd_10658_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-10658.cif.gz | 6.3 KB | ||
Others | emd_10658_half_map_1.map.gz emd_10658_half_map_2.map.gz | 226.5 MB 226.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10658 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10658 | HTTPS FTP |
-Validation report
Summary document | emd_10658_validation.pdf.gz | 1017.4 KB | Display | EMDB validaton report |
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Full document | emd_10658_full_validation.pdf.gz | 1017 KB | Display | |
Data in XML | emd_10658_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_10658_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10658 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10658 | HTTPS FTP |
-Related structure data
Related structure data | 6xzcMC 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_10658.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharped map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.058 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_10658_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Map A
File | emd_10658_half_map_1.map | ||||||||||||
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Annotation | Map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Map B
File | emd_10658_half_map_2.map | ||||||||||||
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Annotation | Map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : EspB Heptameric complex
Entire | Name: EspB Heptameric complex |
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Components |
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-Supramolecule #1: EspB Heptameric complex
Supramolecule | Name: EspB Heptameric complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mycobacterium tuberculosis H37Rv (bacteria) |
Molecular weight | Theoretical: 329 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 tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv |
Molecular weight | Theoretical: 47.637527 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MTQSQTVTVD QQEILNRANE VEAPMADPPT DVPITPCELT AAKNAAQQLV LSADNMREYL AAGAKERQRL ATSLRNAAKA YGEVDEEAA TALDNDGEGT VQAESAGAVG GDSSAELTDT PRVATAGEPN FMDLKEAARK LETGDQGASL AHFADGWNTF N LTLQGDVK ...String: MTQSQTVTVD QQEILNRANE VEAPMADPPT DVPITPCELT AAKNAAQQLV LSADNMREYL AAGAKERQRL ATSLRNAAKA YGEVDEEAA TALDNDGEGT VQAESAGAVG GDSSAELTDT PRVATAGEPN FMDLKEAARK LETGDQGASL AHFADGWNTF N LTLQGDVK RFRGFDNWEG DAATACEASL DQQRQWILHM AKLSAAMAKQ AQYVAQLHVW ARREHPTYED IVGLERLYAE NP SARDQIL PVYAEYQQRS EKVLTEYNNK AALEPVNPPK PPPAIKIDPP PPPQEQGLIP GFLMPPSDGS GVTPGTGMPA APM VPPTGS PGGGLPADTA AQLTSAGREA AALSGDVAVK AASLGGGGGG GVPSAPLGSA IGGAESVRPA GAGDIAGLGQ GRAG GGAAL GGGGMGMPMG AAHQGQGGAK SKGSQQEDEA LYTEDRAWTE AVIGNRRRQD SKESK 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 | 5 mg/mL | ||||||
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Buffer | pH: 8 / Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. | ||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV Details: 0.05% fluorinated octylmaltoside was add into protein solution and immediately applied to a freshly glow-discharged holey carbon grid. ). Excess liquid was blotted for 2.3 s using an FEI ...Details: 0.05% fluorinated octylmaltoside was add into protein solution and immediately applied to a freshly glow-discharged holey carbon grid. ). Excess liquid was blotted for 2.3 s using an FEI Vitrobot Mark IV and the sample was plunge frozen in liquid ethane.. | ||||||
Details | This sample was monodiperse |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 2600 / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |