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- PDB-3h01: Structure of the C-terminal Domain of a Putative HIV-1 gp41 Fusio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3h01 | ||||||
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Title | Structure of the C-terminal Domain of a Putative HIV-1 gp41 Fusion Intermediate | ||||||
![]() | Envelope glycoprotein gp160 | ||||||
![]() | 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 | ![]() Dectin-2 family / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.7 KB | Display | ![]() |
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PDB format | ![]() | 44.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.4 KB | Display | ![]() |
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Full document | ![]() | 440.4 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gwoSC ![]() 3h00C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 6844.541 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN (UNP residues 630 to 683) / Mutation: N656L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HXB2 ISOLATE / Gene: env / Production host: ![]() ![]() #2: Chemical | ChemComp-HEZ / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.8M 1,6-hexanediol, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.41 Å / Num. all: 14906 / Num. obs: 14906 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 10.5 / Num. unique all: 1422 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GWO Resolution: 1.7→29.41 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.324 / SU ML: 0.057 Isotropic thermal model: Isotropic with TLS groups assigned for each protein chain Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.112 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 23.359 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→29.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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