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Yorodumi- EMDB-12963: Structure of the outer-membrane core complex (outer ring) from a ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12963 | |||||||||
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Title | Structure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system | |||||||||
Map data | The structure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system | |||||||||
Sample |
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Keywords | Type IV secretion system / F plasmid / outer-membrane core complex / conjugation / MEMBRANE PROTEIN | |||||||||
Function / homology | Pilus assembly TraK / Type-F conjugative transfer system secretin TraK / TraK protein / Type IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Type-F conjugative transfer system secretin TraK / Type IV conjugative transfer system lipoprotein TraV Function and homology information | |||||||||
Biological species | Salmonella enterica (bacteria) / Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Amin H / Ilangovan A / Costa TRD | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Architecture of the outer-membrane core complex from a conjugative type IV secretion system. Authors: Himani Amin / Aravindan Ilangovan / Tiago R D Costa / Abstract: Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double ...Conjugation is one of the most important processes that bacteria utilize to spread antibiotic resistance genes among bacterial populations. Interbacterial DNA transfer requires a large double membrane-spanning nanomachine called the type 4 secretion system (T4SS) made up of the inner-membrane complex (IMC), the outer-membrane core complex (OMCC) and the conjugative pilus. The iconic F plasmid-encoded T4SS has been central in understanding conjugation for several decades, however atomic details of its structure are not known. Here, we report the structure of a complete conjugative OMCC encoded by the pED208 plasmid from E. coli, solved by cryo-electron microscopy at 3.3 Å resolution. This 2.1 MDa complex has a unique arrangement with two radial concentric rings, each having a different symmetry eventually contributing to remarkable differences in protein stoichiometry and flexibility in comparison to other OMCCs. Our structure suggests that F-OMCC is a highly dynamic complex, with implications for pilus extension and retraction during conjugation. | |||||||||
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_12963.map.gz | 391.9 MB | EMDB map data format | |
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Header (meta data) | emd-12963-v30.xml emd-12963.xml | 11 KB 11 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12963_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_12963.png | 63.9 KB | ||
Filedesc metadata | emd-12963.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12963 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12963 | HTTPS FTP |
-Validation report
Summary document | emd_12963_validation.pdf.gz | 663.3 KB | Display | EMDB validaton report |
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Full document | emd_12963_full_validation.pdf.gz | 662.9 KB | Display | |
Data in XML | emd_12963_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_12963_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12963 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12963 | HTTPS FTP |
-Related structure data
Related structure data | 7okoMC 7oknC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12963.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The structure of the outer-membrane core complex (outer ring) from a conjugative type IV secretion system | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 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 : Outer-membrane core complex (outer ring)
Entire | Name: Outer-membrane core complex (outer ring) |
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Components |
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-Supramolecule #1: Outer-membrane core complex (outer ring)
Supramolecule | Name: Outer-membrane core complex (outer ring) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Salmonella enterica (bacteria) |
-Macromolecule #1: Type IV conjugative transfer system lipoprotein TraV
Macromolecule | Name: Type IV conjugative transfer system lipoprotein TraV / type: protein_or_peptide / ID: 1 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica (bacteria) |
Molecular weight | Theoretical: 20.92865 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKITLLLAG SALLLSGCAG VKSSFDCDAT TSDTCMTMTK ANQLARDKAA KQAGKPAAGG LPSLVNLPAT SAVEVPSASR SAVTPPSGT RTVSTTPPVS AGTSAGVNTN TTTSTLTPRP VAGTPVTTTP SSVAYRPVVS VVTPTPSCQN VRCDNPGTVH P QRSRDQIA ...String: MKKITLLLAG SALLLSGCAG VKSSFDCDAT TSDTCMTMTK ANQLARDKAA KQAGKPAAGG LPSLVNLPAT SAVEVPSASR SAVTPPSGT RTVSTTPPVS AGTSAGVNTN TTTSTLTPRP VAGTPVTTTP SSVAYRPVVS VVTPTPSCQN VRCDNPGTVH P QRSRDQIA TVWIAPWVDS DNAFHQPGRV SFVVSPADWV LPARVN UniProtKB: Type IV conjugative transfer system lipoprotein TraV |
-Macromolecule #2: TraB
Macromolecule | Name: TraB / type: protein_or_peptide / ID: 2 / Number of copies: 13 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica (bacteria) |
Molecular weight | Theoretical: 1.128233 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PGMMDSQEFS |
-Macromolecule #3: Type-F conjugative transfer system secretin TraK
Macromolecule | Name: Type-F conjugative transfer system secretin TraK / type: protein_or_peptide / ID: 3 / Number of copies: 26 / Enantiomer: LEVO |
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Source (natural) | Organism: Salmonella enterica subsp. salamae serovar 58:l,z13,z28:z6 (bacteria) |
Molecular weight | Theoretical: 23.312551 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AQSPATISLP QGGQFRLSIS NTDPNMIFIP GDKVTAITAP GGMLADKRLT TAGGVLFTSV ATRTFTIFVE TALGQTFSVV ATPVKGEGR VYRLMSAEPP SRPETRKWET AQAYEKLLIS LNRAVLTGDI PDGYGEVKPL SDGIRLPGGF SVTPLKAWAG D QLRADRYE ...String: AQSPATISLP QGGQFRLSIS NTDPNMIFIP GDKVTAITAP GGMLADKRLT TAGGVLFTSV ATRTFTIFVE TALGQTFSVV ATPVKGEGR VYRLMSAEPP SRPETRKWET AQAYEKLLIS LNRAVLTGDI PDGYGEVKPL SDGIRLPGGF SVTPLKAWAG D QLRADRYE LRNANTWGVA LREQDFWKPG VRAVMFDNNA QTLMGGGRMT VTVIRGNG UniProtKB: Type-F conjugative transfer system secretin TraK |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |