+Open data
-Basic information
Entry | Database: PDB / ID: 5wb1 | ||||||
---|---|---|---|---|---|---|---|
Title | Ligand-free US28 with stabilizing intracellular nanobody | ||||||
Components | Envelope protein US28, nanobody 7 fusion protein | ||||||
Keywords | MEMBRANE PROTEIN / chemokine receptor | ||||||
Function / homology | Function and homology information : / chemokine receptor activity / virus-mediated perturbation of host defense response / chemotaxis / viral envelope / host cell plasma membrane / membrane Similarity search - Function | ||||||
Biological species | Human cytomegalovirus Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.508 Å | ||||||
Authors | Jude, K.M. / Burg, J.S. / Garcia, K.C. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Elife / Year: 2018 Title: Viral GPCR US28 can signal in response to chemokine agonists of nearly unlimited structural degeneracy. Authors: Miles, T.F. / Spiess, K. / Jude, K.M. / Tsutsumi, N. / Burg, J.S. / Ingram, J.R. / Waghray, D. / Hjorto, G.M. / Larsen, O. / Ploegh, H.L. / Rosenkilde, M.M. / Garcia, K.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wb1.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wb1.ent.gz | 71.3 KB | Display | PDB format |
PDBx/mmJSON format | 5wb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/5wb1 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/5wb1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5wb2C 4xt1S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 51827.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human cytomegalovirus, (gene. exp.) Lama glama (llama) Gene: US28 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q80KM9, UniProt: P69333*PLUS |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.95 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 37-41% PEG300, 100 mM MES, pH 6.2-6.6, 100 mM ammonium tartrate in monoolein:cholesterol (9:1) PH range: 6.2-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2015 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 3.49→50 Å / Num. obs: 7426 / % possible obs: 99.2 % / Redundancy: 6.3 % / Biso Wilson estimate: 84.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0221 / Rpim(I) all: 0.0241 / Net I/σ(I): 6.85 |
Reflection shell | Resolution: 3.49→3.58 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.392 / Mean I/σ(I) obs: 0.94 / Num. unique obs: 491 / CC1/2: 0.606 / Rrim(I) all: 1.583 / % possible all: 91.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4XT1 Resolution: 3.508→29.844 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.58
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.508→29.844 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|