[English] 日本語
Yorodumi- PDB-3gwo: Structure of the C-terminal Domain of a Putative HIV-1 gp41 Fusio... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gwo | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the C-terminal Domain of a Putative HIV-1 gp41 Fusion Intermediate | ||||||
Components | Envelope glycoprotein gp160 | ||||||
Keywords | VIRAL PROTEIN / viral membrane fusion / HIV-1 / gp41 / envelope protein / neutralizing antibodies / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Fusion protein / Glycoprotein / Host-virus interaction / Lipoprotein / Membrane / Palmitate / Transmembrane / Viral immunoevasion / Virion | ||||||
Function / homology | Function and homology information Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 lw12.3 isolate | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å | ||||||
Authors | Liu, J. | ||||||
Citation | Journal: J.Virol. / Year: 2010 Title: Role of a putative gp41 dimerization domain in human immunodeficiency virus type 1 membrane fusion. Authors: Liu, J. / Deng, Y. / Li, Q. / Dey, A.K. / Moore, J.P. / Lu, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3gwo.cif.gz | 56 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3gwo.ent.gz | 41.1 KB | Display | PDB format |
PDBx/mmJSON format | 3gwo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/3gwo ftp://data.pdbj.org/pub/pdb/validation_reports/gw/3gwo | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 6845.485 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP residues 630 to 683) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 lw12.3 isolate Strain: HXB2 ISOLATE / Gene: env / Production host: Escherichia coli (E. coli) / References: UniProt: Q70626 #2: Chemical | #3: Chemical | ChemComp-NA / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.13 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 28% Jeffamine M600, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 95 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793,0.9796,0.9681 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2003 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 1.65→20.7 Å / Num. all: 14912 / Num. obs: 14912 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.6 | ||||||||||||
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1470 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.65→20.7 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.953 / SU ML: 0.066 Isotropic thermal model: Isotropic with TLS groups assigned for each protein chain Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.224 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→20.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|