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Yorodumi- EMDB-12707: O-Layer C14 at 2.58A - Local refinement with C14 symmetry of the ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12707 | |||||||||||||||
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Title | O-Layer C14 at 2.58A - Local refinement with C14 symmetry of the O-layer of the outer membrane core complex from the fully-assembled R388 type IV secretion system. | |||||||||||||||
Map data | O-Layer C14 Local Refinement map Sharpened | |||||||||||||||
Sample |
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Function / homology | Function and homology information | |||||||||||||||
Biological species | Escherichia coli (E. coli) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||||||||
Authors | Mace K / Vadakkepat AK / Lukoyanova N / Waksman G | |||||||||||||||
Funding support | United Kingdom, 4 items
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Citation | Journal: Nature / Year: 2022 Title: Cryo-EM structure of a type IV secretion system. Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong ...Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman / Abstract: Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_12707.map.gz | 17.4 MB | EMDB map data format | |
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Header (meta data) | emd-12707-v30.xml emd-12707.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_12707.png | 106.6 KB | ||
Masks | emd_12707_msk_1.map | 18.9 MB | Mask map | |
Others | emd_12707_additional_1.map.gz emd_12707_half_map_1.map.gz emd_12707_half_map_2.map.gz | 17.1 MB 94.4 MB 94.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12707 | HTTPS FTP |
-Related structure data
Related structure data | 7o3jMC 7o3tC 7o3vC 7o41C 7o42C 7o43C 7oiuC 7q1vC 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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-Map
File | Download / File: emd_12707.map.gz / Format: CCP4 / Size: 18.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | O-Layer C14 Local Refinement map Sharpened | ||||||||||||||||||||
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_12707_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: O-Layer C14 Local Refinement map Unsharpened
File | emd_12707_additional_1.map | ||||||||||||
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Annotation | O-Layer C14 Local Refinement map Unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: O-Layer C14 Local Refinement - Half-A
File | emd_12707_half_map_1.map | ||||||||||||
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Annotation | O-Layer C14 Local Refinement - Half-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: O-Layer C14 Local Refinement - Half-B
File | emd_12707_half_map_2.map | ||||||||||||
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Annotation | O-Layer C14 Local Refinement - Half-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Type IV secretion system complex
Entire | Name: Type IV secretion system complexSecretion |
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Components |
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-Supramolecule #1: Type IV secretion system complex
Supramolecule | Name: Type IV secretion system complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: R388 plasmid |
Recombinant expression | Organism: Escherichia coli (E. coli) Recombinant plasmid: pBADM11_trwN/virB1-trwE/virB10Strep_rbstrwD/virB11_rbsHistrwB /virD4 |
Molecular weight | Theoretical: 2.808 MDa |
-Macromolecule #1: TrwE protein
Macromolecule | Name: TrwE protein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / 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 |
-Macromolecule #2: TrwF protein
Macromolecule | Name: TrwF protein / type: protein_or_peptide / ID: 2 / Number of copies: 14 / 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 |
-Macromolecule #3: TrwH protein
Macromolecule | Name: TrwH protein / type: protein_or_peptide / ID: 3 / 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 |
-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 | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: CryoSPARC ab-initio |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: OTHER / Details: Stochastic gradient descent (SGD) |
Final reconstruction | Applied symmetry - Point group: C14 (14 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Number images used: 709769 |