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Yorodumi- EMDB-34716: Cryo-EM structure of ComC bound ComA C17A at inward-facing state -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34716 | |||||||||
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Title | Cryo-EM structure of ComC bound ComA C17A at inward-facing state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ABC transporter / PCAT / MEMBRANE PROTEIN | |||||||||
Biological species | Streptococcus pneumoniae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
Authors | Lin Y / Xin X / Min L | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Structural basis of peptide secretion for Quorum sensing by ComA. Authors: Lin Yu / Xin Xu / Wan-Zhen Chua / Hao Feng / Zheng Ser / Kai Shao / Jian Shi / Yumei Wang / Zongli Li / Radoslaw M Sobota / Lok-To Sham / Min Luo / Abstract: Quorum sensing (QS) is a crucial regulatory mechanism controlling bacterial signalling and holds promise for novel therapies against antimicrobial resistance. In Gram-positive bacteria, such as ...Quorum sensing (QS) is a crucial regulatory mechanism controlling bacterial signalling and holds promise for novel therapies against antimicrobial resistance. In Gram-positive bacteria, such as Streptococcus pneumoniae, ComA is a conserved efflux pump responsible for the maturation and secretion of peptide signals, including the competence-stimulating peptide (CSP), yet its structure and function remain unclear. Here, we functionally characterize ComA as an ABC transporter with high ATP affinity and determined its cryo-EM structures in the presence or absence of CSP or nucleotides. Our findings reveal a network of strong electrostatic interactions unique to ComA at the intracellular gate, a putative binding pocket for two CSP molecules, and negatively charged residues facilitating CSP translocation. Mutations of these residues affect ComA's peptidase activity in-vitro and prevent CSP export in-vivo. We demonstrate that ATP-Mg triggers the outward-facing conformation of ComA for CSP release, rather than ATP alone. Our study provides molecular insights into the QS signal peptide secretion, highlighting potential targets for QS-targeting drugs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34716.map.gz | 59 MB | EMDB map data format | |
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Header (meta data) | emd-34716-v30.xml emd-34716.xml | 15 KB 15 KB | Display Display | EMDB header |
Images | emd_34716.png | 82.5 KB | ||
Filedesc metadata | emd-34716.cif.gz | 5.2 KB | ||
Others | emd_34716_half_map_1.map.gz emd_34716_half_map_2.map.gz | 52 MB 51.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34716 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34716 | HTTPS FTP |
-Validation report
Summary document | emd_34716_validation.pdf.gz | 808.6 KB | Display | EMDB validaton report |
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Full document | emd_34716_full_validation.pdf.gz | 808.2 KB | Display | |
Data in XML | emd_34716_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | emd_34716_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34716 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34716 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34716.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.858 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34716_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34716_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ComC-bound ComA C17A
Entire | Name: ComC-bound ComA C17A |
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Components |
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-Supramolecule #1: ComC-bound ComA C17A
Supramolecule | Name: ComC-bound ComA C17A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Streptococcus pneumoniae (bacteria) |
-Macromolecule #1: ComA
Macromolecule | Name: ComA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptococcus pneumoniae (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKFGKRHYRP QVDQMDAGVA SLAMVFGYYG SYYFLAHLRE LAKTTMDGTT ALGLVKVAEE IGFETRAIKA DMTLFDLPDL TFPFVAHVL KEGKLLHYYV VTGQDKDSIH IADPDPGVKL TKLPRERFEE EWTGVTLFMA PSPDYKPHKE QKNGLLSFIP I LVKQRGLI ...String: MKFGKRHYRP QVDQMDAGVA SLAMVFGYYG SYYFLAHLRE LAKTTMDGTT ALGLVKVAEE IGFETRAIKA DMTLFDLPDL TFPFVAHVL KEGKLLHYYV VTGQDKDSIH IADPDPGVKL TKLPRERFEE EWTGVTLFMA PSPDYKPHKE QKNGLLSFIP I LVKQRGLI ANIVLATLLV TVINIVGSYY LQSIIDTYVP DQMRSTLGII SIGLVIVYIL QQILSYAQEY LLLVLGQRLS ID VILSYIK HVFHLPMSFF ATRRTGEIVS RFTDANSIID ALASTILSIF LDVSTVVIIS LVLFSQNTNL FFMTLLALPI YTV IIFAFM KPFEKMNRDT MEANAVLSSS IIEDINGIET IKSLTSESQR YQKIDKEFVD YLKKSFTYSR AESQQKALKK VAHL LLNVG ILWMGAVLVM DGKMSLGQLI TYNTLLVYFT NPLENIINLQ TKLQTAQVAN NRLNEVYLVA SEFEEKKTVE DLSLM KGDM TFKQVHYKYG YGRDVLSDIN LTVPQGSKVA FVGISGSGKT TLAKMMVNFY DPSQGEISLG GVNLNQIDKK ALRQYI NYL PQQPYVFNGT ILENLLLGAK EGTTQEDILR AVELAEIRED IERMPLNYQT ELTSDGAGIS GGQRQRIALA RALLTDA PV IILDEATSSL DILTEKRIVD NLIALDKTLI FIAHRLTIAE RTEKVVVLDQ GKIVEEGKHA DLLAQGGFYA HLVNS |
-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: 7.5 / Details: 25 mM Tris, pH 7.5, 150 mM NaCl, 2 mM DTT |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25560 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |