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- EMDB-19479: I-Layer C16 at 2.69A - Local refinement with C16 symmetry of the ... -
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Open data
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Basic information
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Title | I-Layer C16 at 2.69A - Local refinement with C16 symmetry of the I-layer of the outer membrane core complex from the fully-assembled R388 type IV secretion system. | |||||||||||||||
![]() | I-Layer C16 at 2.69A - Unsharpen | |||||||||||||||
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![]() | type IV secretion system type 4 secretion system T4SS I-layer core complex outer membrane complex R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB10 VirB9 TrwE TrwF / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.69 Å | |||||||||||||||
![]() | Mace K / Waksman G | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of a conjugative type IV secretion system suggests a molecular switch regulating pilus biogenesis. Authors: Kévin Macé / Gabriel Waksman / ![]() ![]() Abstract: Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. ...Conjugative type IV secretion systems (T4SS) mediate bacterial conjugation, a process that enables the unidirectional exchange of genetic materials between a donor and a recipient bacterial cell. Bacterial conjugation is the primary means by which antibiotic resistance genes spread among bacterial populations (Barlow 2009; Virolle et al, 2020). Conjugative T4SSs form pili: long extracellular filaments that connect with recipient cells. Previously, we solved the cryo-electron microscopy (cryo-EM) structure of a conjugative T4SS. In this article, based on additional data, we present a more complete T4SS cryo-EM structure than that published earlier. Novel structural features include details of the mismatch symmetry within the OMCC, the presence of a fourth VirB8 subunit in the asymmetric unit of both the arches and the inner membrane complex (IMC), and a hydrophobic VirB5 tip in the distal end of the stalk. Additionally, we provide previously undescribed structural insights into the protein VirB10 and identify a novel regulation mechanism of T4SS-mediated pilus biogenesis by this protein, that we believe is a key checkpoint for this process. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 48.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.1 KB 18.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 73.8 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() ![]() | 91.4 MB 93.7 MB 93.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rt5MC ![]() 8rt4C ![]() 8rt6C ![]() 8rt7C ![]() 8rt8C ![]() 8rt9C ![]() 8rtaC ![]() 8rtbC ![]() 8rtdC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | I-Layer C16 at 2.69A - Unsharpen | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.067 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: I-Layer C16 at 2.69A - Sharpened deepEMhancer
File | emd_19479_additional_1.map | ||||||||||||
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Annotation | I-Layer C16 at 2.69A - Sharpened_deepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-A
File | emd_19479_half_map_1.map | ||||||||||||
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Annotation | Half-A | ||||||||||||
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Density Histograms |
-Half map: Half-B
File | emd_19479_half_map_2.map | ||||||||||||
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Annotation | Half-B | ||||||||||||
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Density Histograms |
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Sample components
-Entire : the outer membrane core complex from the fully-assembled R388 typ...
Entire | Name: the outer membrane core complex from the fully-assembled R388 type IV secretion system |
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Components |
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-Supramolecule #1: the outer membrane core complex from the fully-assembled R388 typ...
Supramolecule | Name: the outer membrane core complex from the fully-assembled R388 type IV secretion system type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: TrwE protein
Macromolecule | Name: TrwE protein / type: protein_or_peptide / ID: 1 / Details: Sequence from conjugative plasmid R388 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 42.443785 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MFGRKKGDVI DAGAELERAE QERIEGEYGA SELASERRPH TPGARTLLMV LLCVIAVVLV TLSYKAYKVR GVVEDDDAQP QQVVRQVIP GYTPRPIRPE PENVPEPPQP TTSVPAIQPA PVTQPVRPQP TGPREKTPYE LARERMLRSG LTAGSGGGED L PRPQGGDV ...String: MFGRKKGDVI DAGAELERAE QERIEGEYGA SELASERRPH TPGARTLLMV LLCVIAVVLV TLSYKAYKVR GVVEDDDAQP QQVVRQVIP GYTPRPIRPE PENVPEPPQP TTSVPAIQPA PVTQPVRPQP TGPREKTPYE LARERMLRSG LTAGSGGGED L PRPQGGDV PAGGLMGGGG GGGELAEKLQ PMRLSGSSAG RLGNRDMLIT QGTQLDCVLE TRLVTTQPGM TTCHLTRDVY ST SGRVVLL DRGSKVVGFY QGGLRQGQAR IFVQWSRIET PSGVVINLDS PGTGPLGEAG LGGWIDRHFW ERFGGAIMIS LIG DLGDWA SRQGSRQGDN SIQFSNTANG VESAAAEALR NSINIPPTLY KNQGERVNIL VARDLDFSDV YSLESIPTK UniProtKB: TrwE protein |
-Macromolecule #2: TrwF protein
Macromolecule | Name: TrwF protein / type: protein_or_peptide / ID: 2 / Details: Sequence from conjugative plasmid R388 / Number of copies: 16 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 29.749586 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKKLAIVALL ASLHAVPALA LDVPSSSRYD HRIRYVTYNP ADVVQVDTVL GVATHIMLEE GEQYLTHAFG DSEAYAFARK GRHIFIKPQ AELANTNLIV VTDRRSYKFR LQMRNDRNGA MYELAFRYPD TQARQTREAN ARAAVEAAFE QRVGAYYNLK Y MMSGDKDI ...String: MKKLAIVALL ASLHAVPALA LDVPSSSRYD HRIRYVTYNP ADVVQVDTVL GVATHIMLEE GEQYLTHAFG DSEAYAFARK GRHIFIKPQ AELANTNLIV VTDRRSYKFR LQMRNDRNGA MYELAFRYPD TQARQTREAN ARAAVEAAFE QRVGAYYNLK Y MMSGDKDI APVNAWDDGR FTYFKFSANA DLPSIYFVDA EGNESLVPRT TVGSSNNIIA VHKVNPKWMI RLGNRALAIF NE AYDPNGV PNDTGTASPA VRRVNKGGN UniProtKB: TrwF protein |
-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: 7.6 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.3000000000000003 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |