[English] 日本語
Yorodumi- PDB-1df4: INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1df4 | ||||||
---|---|---|---|---|---|---|---|
Title | INTERACTIONS BETWEEN HIV-1 GP41 CORE AND DETERGENTS AND THEIR IMPLICATIONS FOR MEMBRANE FUSION | ||||||
Components | HIV-1 ENVELOPE GLYCOPROTEIN GP41 | ||||||
Keywords | VIRAL PROTEIN / HIV-1 / GP41 / MEMBRANE FUSION / PROTEIN-DETERGENT INTERACTION | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å | ||||||
Authors | Shu, W. / Ji, H. / Lu, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Interactions between HIV-1 gp41 core and detergents and their implications for membrane fusion. Authors: Shu, W. / Ji, H. / Lu, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1df4.cif.gz | 24.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1df4.ent.gz | 15.5 KB | Display | PDB format |
PDBx/mmJSON format | 1df4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1df4_validation.pdf.gz | 364.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1df4_full_validation.pdf.gz | 365.1 KB | Display | |
Data in XML | 1df4_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 1df4_validation.cif.gz | 3.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/1df4 ftp://data.pdbj.org/pub/pdb/validation_reports/df/1df4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 7879.753 Da / Num. of mol.: 1 Fragment: RESIDUES 1 - 34 AND 41 - 68 CONNECTED BY A SIX-RESIDUE LINKER (SER-GLY-GLY-ARG- GLY-GLY) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus Description: RECOMBINANT GP41 WITH LINKER (SER-GLY-GLY- ARG-GLY-GLY) BETWEEN TWO FRAGMENTS Production host: Escherichia coli (E. coli) / References: UniProt: P04578 |
---|---|
#2: Water | ChemComp-HOH / |
Compound details | IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - ...IN THE STRUCTURE, SEQUENCE 1 - 34 IS FROM GP41 RESIDUES 546 - 579 (IN GP160 NUMBERING SYSTEM), 35 - 40 IS AN ARTIFICIAL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.81 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: SODIUM CITRATE, AMMONIUM DIHYDROGEN PHOSPHATE, BETA-OG, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 130 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.71069 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71069 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→16.5 Å / Num. all: 11818 / Num. obs: 11818 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.028 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.45→1.51 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.125 / % possible all: 96.9 |
Reflection | *PLUS Num. measured all: 43163 |
Reflection shell | *PLUS % possible obs: 96.9 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.45→16.5 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→16.5 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|