+Open data
-Basic information
Entry | Database: PDB / ID: 3vh7 | ||||||
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Title | Structure of HIV-1 gp41 NHR/fusion inhibitor complex P21 | ||||||
Components |
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Keywords | MEMBRANE PROTEIN/INHIBITOR / 6-helix bundle / membrane fusion inhibition / MEMBRANE PROTEIN-INHIBITOR complex | ||||||
Function / homology | Function and homology information host cell periphery / CD4 receptor binding / 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 / host cell perinuclear region of cytoplasm / viral protein processing ...host cell periphery / CD4 receptor binding / 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 / host cell perinuclear region of cytoplasm / 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 / protein-containing complex binding / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.019 Å | ||||||
Authors | Yao, X. / Waltersperger, S. / Wang, M.T. / Cui, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural basis of potent and broad HIV-1 fusion inhibitor CP32M Authors: Yao, X. / Chong, H. / Zhang, C. / Qiu, Z. / Qin, B. / Han, R. / Waltersperger, S. / Wang, M.T. / He, Y. / Cui, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vh7.cif.gz | 110 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vh7.ent.gz | 87.3 KB | Display | PDB format |
PDBx/mmJSON format | 3vh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3vh7_validation.pdf.gz | 468.9 KB | Display | wwPDB validaton report |
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Full document | 3vh7_full_validation.pdf.gz | 472.9 KB | Display | |
Data in XML | 3vh7_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | 3vh7_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/3vh7 ftp://data.pdbj.org/pub/pdb/validation_reports/vh/3vh7 | HTTPS FTP |
-Related structure data
Related structure data | 3vgyC 3f4yS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 6413.350 Da / Num. of mol.: 3 / Fragment: NHR (UNP RESIDUES (546-588) / Source method: obtained synthetically / Details: This sequence occurs naturally. / Source: (synth.) Human immunodeficiency virus type 1 / References: UniProt: P03375 #2: Protein/peptide | Mass: 4295.733 Da / Num. of mol.: 3 / Source method: obtained synthetically Details: This sequence does not occur naturally, but designed based on sequence of HIV-1 gp41 CHR 621-652. #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.99 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M MgCl2, 0.1M Sodium acetate, 25% PEG 400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2011 |
Radiation | Monochromator: Bartels Monochromator Crystal Type Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.019→42.607 Å / Num. obs: 14977 / % possible obs: 90.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 1.97 % / Rmerge(I) obs: 0.084 / Rsym value: 0.085 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.02→2.14 Å / Redundancy: 1.24 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 1.18 / Num. unique all: 3185 / Rsym value: 0.764 / % possible all: 63.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3F4Y Resolution: 2.019→42.607 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 28.02 / Stereochemistry target values: ML Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.303 Å2 / ksol: 0.385 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.019→42.607 Å
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Refine LS restraints |
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LS refinement shell |
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