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Yorodumi- EMDB-5287: The single particle reconstruction of detergent-solubilized full-... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5287 | |||||||||
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Title | The single particle reconstruction of detergent-solubilized full-length human Toll-like receptor 5 | |||||||||
Map data | This is the volume of wildtype TLR5. | |||||||||
Sample |
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Keywords | Toll-like receptor 5 / full-length protein | |||||||||
Function / homology | Function and homology information Toll Like Receptor 5 (TLR5) Cascade / toll-like receptor 5 signaling pathway / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / interleukin-1 receptor binding / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / cellular response to mechanical stimulus ...Toll Like Receptor 5 (TLR5) Cascade / toll-like receptor 5 signaling pathway / MyD88 deficiency (TLR5) / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / interleukin-1 receptor binding / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / cellular response to mechanical stimulus / transmembrane signaling receptor activity / signaling receptor activity / inflammatory response / innate immune response / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 26.0 Å | |||||||||
Authors | Zhou K / Kanai R / Lee P / Wang HW / Modis Y | |||||||||
Citation | Journal: J Struct Biol / Year: 2012 Title: Toll-like receptor 5 forms asymmetric dimers in the absence of flagellin. Authors: Kaifeng Zhou / Ryuta Kanai / Phong Lee / Hong-Wei Wang / Yorgo Modis / Abstract: The structure of full-length human TLR5 determined by electron microscopy single-particle image reconstruction at 26Å resolution shows that TLR5 forms an asymmetric homodimer via ectodomain ...The structure of full-length human TLR5 determined by electron microscopy single-particle image reconstruction at 26Å resolution shows that TLR5 forms an asymmetric homodimer via ectodomain interactions. The structure shows that like TLR9, TLR5 dimerizes in the absence of ligand. The asymmetry of the dimer suggests that TLR5 may recognize two flagellin molecules cooperatively to establish an optimal flagellin response threshold. A TLR5 homology model was generated and fitted into the electron microscopy structure. All seven predicted N-linked glycosylation sites are exposed on the molecular surface, away from the dimer interface. Glycosylation at the first five sites was confirmed by tandem mass spectrometry. Two aspartate residues proposed to interact with flagellin (Asp294 and Asp366) are sterically occluded by a glycan at position 342. In contrast, the central region of the ectodomains near the dimer interface is unobstructed by glycans. Ligand binding in this region would be consistent with the ligand binding sites of other TLRs. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5287.map.gz | 3.4 MB | EMDB map data format | |
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Header (meta data) | emd-5287-v30.xml emd-5287.xml | 9.8 KB 9.8 KB | Display Display | EMDB header |
Images | emd_5287_1.png | 225.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5287 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5287 | HTTPS FTP |
-Validation report
Summary document | emd_5287_validation.pdf.gz | 294.6 KB | Display | EMDB validaton report |
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Full document | emd_5287_full_validation.pdf.gz | 294.1 KB | Display | |
Data in XML | emd_5287_validation.xml.gz | 5.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5287 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5287 | HTTPS FTP |
-Related structure data
Related structure data | 3j0aMC 5288C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5287.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the volume of wildtype TLR5. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Full-length toll-like receptor 5
Entire | Name: Full-length toll-like receptor 5 |
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Components |
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-Supramolecule #1000: Full-length toll-like receptor 5
Supramolecule | Name: Full-length toll-like receptor 5 / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: dimer / Number unique components: 2 |
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Molecular weight | Experimental: 200 KDa / Theoretical: 200 KDa / Method: gel filtration |
-Macromolecule #1: Toll-like receptor
Macromolecule | Name: Toll-like receptor / type: protein_or_peptide / ID: 1 / Name.synonym: TLR5 / Number of copies: 2 / Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human / Cell: Sf9 insect cells / Organelle: membrane / Location in cell: plasma membrane |
Molecular weight | Experimental: 200 KDa / Theoretical: 200 KDa |
Recombinant expression | Organism: Sf9 insect cells / Recombinant plasmid: pAcGP67-A |
Sequence | InterPro: Toll-like receptor |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.005 mg/mL |
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Buffer | pH: 7.5 / Details: 10 mM TEA, 0.15 M NaCl |
Staining | Type: NEGATIVE Details: The protein solution was applied onto a thin-carbon-covered holey carbon copper grid and negatively stained in 1% uranyl-formate solution for 1 minute. |
Grid | Details: thin carbon covered home-made holey carbon on 400 mesh copper grid |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI 12 |
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Date | Aug 1, 2010 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 50 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: SIDE ENTRY, EUCENTRIC |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC SPIDER Details: Final maps were calculated from all the particles by back-projection reconstruction. Number images used: 4241 |
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Final two d classification | Number classes: 100 |