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Yorodumi- EMDB-19482: Conformation-C OMCC at 3.05A - Refinement without symmetry of the... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19482 | |||||||||||||||
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Title | Conformation-C OMCC at 3.05A - Refinement without symmetry of the outer membrane core complex from the fully-assembled R388 type IV secretion system. | |||||||||||||||
Map data | OMCC_Conformation-C _ Unsharpened | |||||||||||||||
Sample |
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Keywords | type IV secretion system type 4 secretion system T4SS OMCC Conformation-C core complex outer membrane complex R388 plasmid conjugation bacterial secretion secretion secretion system protein complex VirB10 VirB9 VirB7 TrwE TrwF TrwH / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||||||||
Authors | Mace K / Waksman G | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: EMBO J / Year: 2024 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 | emd_19482.map.gz | 50.3 MB | EMDB map data format | |
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Header (meta data) | emd-19482-v30.xml emd-19482.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19482_fsc.xml | 10 KB | Display | FSC data file |
Images | emd_19482.png | 112.9 KB | ||
Masks | emd_19482_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-19482.cif.gz | 5.8 KB | ||
Others | emd_19482_additional_1.map.gz emd_19482_half_map_1.map.gz emd_19482_half_map_2.map.gz | 91.1 MB 95.2 MB 95.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19482 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19482 | HTTPS FTP |
-Validation report
Summary document | emd_19482_validation.pdf.gz | 987.1 KB | Display | EMDB validaton report |
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Full document | emd_19482_full_validation.pdf.gz | 986.7 KB | Display | |
Data in XML | emd_19482_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_19482_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19482 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19482 | HTTPS FTP |
-Related structure data
Related structure data | 8rt8MC 8rt4C 8rt5C 8rt6C 8rt7C 8rt9C 8rtaC 8rtbC 8rtdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_19482.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | OMCC_Conformation-C _ Unsharpened | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
File | emd_19482_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: OMCC Conformation-C Sharpened
File | emd_19482_additional_1.map | ||||||||||||
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Annotation | OMCC_Conformation-C _ Sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-B
File | emd_19482_half_map_1.map | ||||||||||||
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Annotation | Half-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-A
File | emd_19482_half_map_2.map | ||||||||||||
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Annotation | Half-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Conformation-C of the outer membrane core complex from the fully-...
Entire | Name: Conformation-C of 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: Conformation-C of the outer membrane core complex from the fully-...
Supramolecule | Name: Conformation-C of 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: Escherichia coli (E. coli) |
-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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 42.443785 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 29.749586 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
-Macromolecule #3: TrwH protein
Macromolecule | Name: TrwH protein / type: protein_or_peptide / ID: 3 / Details: Sequence from conjugative plasmid R388 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 5.089048 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKTIIFAILM TGLLSACASA PKPKQPSDFN REPVNKTVPV EIQRGAL UniProtKB: TrwH protein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |