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- EMDB-19478: O-Layer C14 at 2.46A - Local refinement with C14 symmetry of the ... -
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Open data
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Basic information
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Title | O-Layer C14 at 2.46A - Local refinement with C14 symmetry of the O-layer of the outer membrane core complex from the fully-assembled R388 type IV secretion system. | |||||||||||||||
![]() | OMCC_O-layer_C14 Unsharpen | |||||||||||||||
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![]() | type IV secretion system type 4 secretion system T4SS O-layer 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 | ![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.46 Å | |||||||||||||||
![]() | Mace K / Waksman G | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of a conjugative type 4 secretion system identifies a molecular switch regulating conjugative pilus biogenesis Authors: Mace K / Waksman G | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.1 KB 19.1 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.9 KB | Display | ![]() |
Images | ![]() | 94.7 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.8 KB | ||
Others | ![]() ![]() ![]() | 91.1 MB 94 MB 94 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 783.8 KB | Display | ![]() |
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Full document | ![]() | 783.3 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rt4MC ![]() 8rt5C ![]() 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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Related items in Molecule of the Month |
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Map
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Annotation | OMCC_O-layer_C14 Unsharpen | ||||||||||||||||||||||||||||||||||||
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
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Projections & Slices |
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Density Histograms |
-Additional map: OMCC O-layer C14 Sharpen deepEMhancer
File | emd_19478_additional_1.map | ||||||||||||
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Annotation | OMCC_O-layer_C14 Sharpen_deepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: OMCC O-layer C14 Half-B
File | emd_19478_half_map_1.map | ||||||||||||
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Annotation | OMCC_O-layer_C14 Half-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: OMCC O-layer C14 Half-A
File | emd_19478_half_map_2.map | ||||||||||||
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Annotation | OMCC_O-layer_C14 Half-A | ||||||||||||
Projections & Slices |
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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: 14 / 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: 14 / 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 |
-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: ![]() ![]() |
Molecular weight | Theoretical: 5.089048 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKTIIFAILM TGLLSACASA PKPKQPSDFN REPVNKTVPV EIQRGAL UniProtKB: TrwH 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 |