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- EMDB-12962: Structure of the outer-membrane core complex (inner ring) from a ... -
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Basic information
Entry | Database: EMDB / ID: EMD-12962 | |||||||||
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Title | Structure of the outer-membrane core complex (inner ring) from a conjugative type IV secretion system | |||||||||
![]() | Structure of the outer-membrane core complex (inner ring) from a conjugative type IV secretion system | |||||||||
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Function / homology | Type IV conjugative transfer system protein TraV / Type IV conjugative transfer system lipoprotein (TraV) / Type IV conjugative transfer system lipoprotein TraV![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | |||||||||
![]() | Amin H / Ilangovan A / Costa TRD | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 392 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.6 KB 10.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.9 KB | Display | ![]() |
Images | ![]() | 86.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 363.5 KB | Display | ![]() |
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Full document | ![]() | 363.1 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 20.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7oknMC ![]() 7okoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the outer-membrane core complex (inner 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
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Sample components
-Entire : Outer-membrane core complex (inner ring)
Entire | Name: Outer-membrane core complex (inner ring) |
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Components |
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-Supramolecule #1: Outer-membrane core complex (inner ring)
Supramolecule | Name: Outer-membrane core complex (inner ring) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: TraB
Macromolecule | Name: TraB / type: protein_or_peptide / ID: 1 / Details: TraB / Number of copies: 17 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 48.802102 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MANVNKVVRR RQVALLIALV LGIGAGGAGT WMVSEMNLKK APPAKAPKGE PAPDMTGVVN QSFDNKVQRS AIAEAQRLNK ETQTEIKKL RTEMGLVSRD LKGSQDRIRE LEDQNQLLQT QLEAGKNFDS LSAEPLPGAL ASQGKPAPAG NVPPPTSFWP A GGGQAPAA ...String: MANVNKVVRR RQVALLIALV LGIGAGGAGT WMVSEMNLKK APPAKAPKGE PAPDMTGVVN QSFDNKVQRS AIAEAQRLNK ETQTEIKKL RTEMGLVSRD LKGSQDRIRE LEDQNQLLQT QLEAGKNFDS LSAEPLPGAL ASQGKPAPAG NVPPPTSFWP A GGGQAPAA PVMTPIQRPG MMDSQEFSLP DTGPKKPRFP WISSGSFVEA IVVEGADANA SVTGDKNTAP MQLRLTGKVQ MP NDEEFDL TGCFVTLEAW GDVSSERAIV RSRSISCKLG DDDIDQKIAG HVSFMGKNGI KGEVVMRNGQ ILLYAGGAGF LDG IGKGIE KASSTTVGVG ATASMSAADI GQAGLGGGVS SAAKTLSDYY IKRAEQYHPV IPIGAGNEVT LVFQDGFQLE TLEE ARAKA AARKKQNQPS ASSTPAAMPG NTPDMLKQLQ DFRVGDTVDP ATGQVVTQWS HPQFEK |
-Macromolecule #2: Type IV conjugative transfer system lipoprotein TraV
Macromolecule | Name: Type IV conjugative transfer system lipoprotein TraV / type: protein_or_peptide / ID: 2 / Details: TraV / Number of copies: 17 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 20.92865 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |