+Open data
-Basic information
Entry | Database: PDB / ID: 3v44 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal fragment of zebrafish TLR5 | ||||||
Components | Toll-like receptor 5b and variable lymphocyte receptor B.61 chimeric protein | ||||||
Keywords | IMMUNE SYSTEM / flagellin / innate immunity / Leucine-rich repeat / innate immune receptor | ||||||
Function / homology | Function and homology information toll-like receptor 5 signaling pathway / activation of immune response / toll-like receptor signaling pathway / transmembrane signaling receptor activity / signaling receptor activity / inflammatory response / innate immune response / membrane Similarity search - Function | ||||||
Biological species | Danio rerio (zebrafish) Eptatretus burgeri (inshore hagfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Yoon, S.I. / Hong, H. / Wilson, I.A. | ||||||
Citation | Journal: Science / Year: 2012 Title: Structural basis of TLR5-flagellin recognition and signaling. Authors: Yoon, S.I. / Kurnasov, O. / Natarajan, V. / Hong, M. / Gudkov, A.V. / Osterman, A.L. / Wilson, I.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3v44.cif.gz | 168 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3v44.ent.gz | 137.5 KB | Display | PDB format |
PDBx/mmJSON format | 3v44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/3v44 ftp://data.pdbj.org/pub/pdb/validation_reports/v4/3v44 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 45719.047 Da / Num. of mol.: 1 Fragment: zebrafish Toll-like receptor 5b (UNP residues 22-342) and hagfish variable lymphocyte receptor B.61 (UNP residues 126-200) Mutation: V24E, L124V, Q159K, R227K, S229T, D334N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish), (gene. exp.) Eptatretus burgeri (inshore hagfish) Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B3DIN1, UniProt: Q4G1L2 | ||
---|---|---|---|
#2: Sugar | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.16 Å3/Da / Density % sol: 76.15 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% MPD, 0.1 M Hepes pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→20 Å / Num. all: 22951 / Num. obs: 22951 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.83→2.93 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.544 / % possible all: 98.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.635 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.831→2.903 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|