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Yorodumi- EMDB-4118: CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4118 | |||||||||
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Title | CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A | |||||||||
Map data | PLY pore complex | |||||||||
Sample |
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Keywords | Bacterial toxins / pore complex / cryoEM structure / cholesterol-dependent cytolysin / Pneumolysin / membrane pore / TOXIN | |||||||||
Function / homology | Function and homology information cholesterol binding / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane Similarity search - Function | |||||||||
Biological species | Streptococcus pneumoniae (bacteria) / Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | van Pee K / Neuhaus A | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Elife / Year: 2017 Title: CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin. Authors: Katharina van Pee / Alexander Neuhaus / Edoardo D'Imprima / Deryck J Mills / Werner Kühlbrandt / Özkan Yildiz / Abstract: Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of ...Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of , by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane. | |||||||||
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_4118.map.gz | 19.1 MB | EMDB map data format | |
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Header (meta data) | emd-4118-v30.xml emd-4118.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4118_fsc.xml | 12.4 KB | Display | FSC data file |
Images | emd_4118.png | 148.8 KB | ||
Filedesc metadata | emd-4118.cif.gz | 5.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4118 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4118 | HTTPS FTP |
-Validation report
Summary document | emd_4118_validation.pdf.gz | 265.1 KB | Display | EMDB validaton report |
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Full document | emd_4118_full_validation.pdf.gz | 264.2 KB | Display | |
Data in XML | emd_4118_validation.xml.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4118 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4118 | HTTPS FTP |
-Related structure data
Related structure data | 5ly6MC 5aoeC 5aofC 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_4118.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PLY pore complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pneumolysin pore complex
Entire | Name: Pneumolysin pore complex |
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Components |
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-Supramolecule #1: Pneumolysin pore complex
Supramolecule | Name: Pneumolysin pore complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Streptococcus pneumoniae (bacteria) |
Molecular weight | Theoretical: 2.2 MDa |
-Macromolecule #1: Pneumolysin
Macromolecule | Name: Pneumolysin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria) |
Molecular weight | Theoretical: 52.866066 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MANKAVNDFI LAMNYDKKKL LTHQGESIEN RFIKEGNQLP DEFVVIERKK RSLSTNTSDI SVTATNDSRL YPGALLVVDE TLLENNPTL LAVDRAPMTY SIDLPGLASS DSFLQVEDPS NSSVRGAVND LLAKWHQDYG QVNNVPARMQ YEKITAHSME Q LKVKFGSD ...String: MANKAVNDFI LAMNYDKKKL LTHQGESIEN RFIKEGNQLP DEFVVIERKK RSLSTNTSDI SVTATNDSRL YPGALLVVDE TLLENNPTL LAVDRAPMTY SIDLPGLASS DSFLQVEDPS NSSVRGAVND LLAKWHQDYG QVNNVPARMQ YEKITAHSME Q LKVKFGSD FEKAANSLDI DFNAVHSGEK QIQIVNFKQI YYTVSVDAVK NPGDVFQDTV TVEDLKQRGI SAERPLVYIS SV AYGRQVY LKLETTSKSD EVQAAFEAAI LGVKVAPQTQ WKQILDNTEV KAVILGGDPS SGARVVTGKV DMVEDLIQEG SRF TADHPG LPISYTTSFL RDNVVATFQN STDYVETKVT AYRNGDLLLD HSGAYVAQYY ITWDELSYDH QGKEVLTPKA WDRN GQDLT AHFTTSIPLK GNVRNLSVKI RECTGLAWEW WRTVYEKTDL PLVRKRTISI WGTTLYPQVE DKVEND UniProtKB: Pneumolysin |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 6.0 sec. / Average electron dose: 1.02 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |