[English] 日本語
![](img/lk-miru.gif)
- PDB-8aic: X-ray structure of the receptor binding domain of Env glycoprotei... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8aic | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the receptor binding domain of Env glycoprotein of Simian Foamy virus | ||||||
![]() | Envelope glycoprotein gp130 | ||||||
![]() | VIRAL PROTEIN / Receptor binding domain | ||||||
Function / homology | Foamy virus envelope protein / Foamy virus envelope protein / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane / Envelope glycoprotein gp130![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Backovic, M. / Fernandez, I. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells. Authors: Fernandez, I. / Dynesen, L.T. / Coquin, Y. / Pederzoli, R. / Brun, D. / Haouz, A. / Gessain, A. / Rey, F.A. / Buseyne, F. / Backovic, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 374.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 260.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 27.8 KB | Display | |
Data in CIF | ![]() | 38.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8aezC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
-Protein / Non-polymers , 2 types, 109 molecules AB![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 40288.566 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #7: Water | ChemComp-HOH / | |
---|
-Sugars , 5 types, 13 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.25 Å3/Da / Density % sol: 76.55 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M ammonium tartarate, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 19, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→46.73 Å / Num. obs: 40619 / % possible obs: 99.58 % / Redundancy: 21.6 % / Biso Wilson estimate: 70.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.04364 / Net I/σ(I): 13.35 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 21.6 % / Rmerge(I) obs: 1.705 / Num. unique obs: 4041 / CC1/2: 0.689 / Rpim(I) all: 0.3719 / % possible all: 99.14 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Related deposition D_1292124233 Resolution: 2.8→46.73 Å / SU ML: 0.4391 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9352 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→46.73 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 37.3339561032 Å / Origin y: 43.2539780996 Å / Origin z: 29.6017111713 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |