+Open data
-Basic information
Entry | Database: PDB / ID: 1g2c | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN RESPIRATORY SYNCYTIAL VIRUS FUSION PROTEIN CORE | ||||||
Components | (FUSION PROTEIN (F)) x 2 | ||||||
Keywords | VIRAL PROTEIN / membrane fusion / pneumovirus / HRSV | ||||||
Function / homology | Function and homology information positive regulation of syncytium formation by virus / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / membrane => GO:0016020 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane Similarity search - Function | ||||||
Biological species | Human respiratory syncytial virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Zhao, X. / Singh, M. / Malashkevich, V.N. / Kim, P.S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Structural characterization of the human respiratory syncytial virus fusion protein core. Authors: Zhao, X. / Singh, M. / Malashkevich, V.N. / Kim, P.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1g2c.cif.gz | 221.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1g2c.ent.gz | 182.4 KB | Display | PDB format |
PDBx/mmJSON format | 1g2c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2c ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2c | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
3 |
| ||||||||||
4 |
| ||||||||||
Unit cell |
| ||||||||||
Details | The biological assembly is a trimer of heterodimer constructed from chain A, B, C,D,E,F |
-Components
#1: Protein | Mass: 5653.654 Da / Num. of mol.: 12 / Fragment: RESIDUES 153-209, HRSV F1 HEPTAD REPEAT Source method: isolated from a genetically manipulated source Details: FIRST HEPTAD REPEAT / Source: (gene. exp.) Human respiratory syncytial virus / Genus: Pneumovirus / Strain: RSS-2 / Gene: HRSV F / Plasmid: PQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P11209 #2: Protein/peptide | Mass: 4873.347 Da / Num. of mol.: 12 / Fragment: RESIDUES 476-520, HRSV F1 HEPTAD REPEAT Source method: isolated from a genetically manipulated source Details: SECOND HEPTAD REPEAT / Source: (gene. exp.) Human respiratory syncytial virus / Genus: Pneumovirus / Strain: RSS-2 / Gene: HRSV F / Plasmid: PQE9 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE / References: UniProt: P11209 #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.9 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, Tris-HCl, Li2SO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9816 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9816 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35 Å / Num. all: 62470 / Num. obs: 56973 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / Redundancy: 1.3 % / Biso Wilson estimate: 40.37 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2 % / Rmerge(I) obs: 0.24 / Num. unique all: 6224 / % possible all: 64.7 |
Reflection | *PLUS Num. measured all: 119905 |
Reflection shell | *PLUS % possible obs: 64.7 % |
-Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: modified polyser SV5 Resolution: 2.3→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1137175.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
| ||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.95 Å2 / ksol: 0.283 e/Å3 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.6 Å2
| ||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
| ||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10.2 % | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 54.6 Å2 | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.352 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.292 |