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- PDB-3mko: Crystal Structure of the Lymphocytic Choriomeningitis Virus Membr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mko | ||||||
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Title | Crystal Structure of the Lymphocytic Choriomeningitis Virus Membrane Fusion Glycoprotein GP2 in its Postfusion Conformation | ||||||
![]() | Glycoprotein C | ||||||
![]() | VIRAL PROTEIN / Trimeric coiled-coil | ||||||
Function / homology | ![]() host cell Golgi membrane / receptor-mediated endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Igonet, S. / Vaney, M.C. / Rey, F.A. | ||||||
![]() | ![]() Title: X-ray structure of the arenavirus glycoprotein GP2 in its postfusion hairpin conformation Authors: Igonet, S. / Vaney, M.C. / Vonhrein, C. / Bricogne, G. / Stura, E.A. / Hengartner, H. / Eschli, B. / Rey, F.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 34.5 KB | Display | ![]() |
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PDB format | ![]() | 26.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.2 KB | Display | ![]() |
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Full document | ![]() | 454.8 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16121.222 Da / Num. of mol.: 1 / Fragment: Ectodomain / Mutation: C316S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-IUM / | #5: Water | ChemComp-HOH / | Sequence details | THESE FOUR RESIDUES CORRESPOND | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 15% MPD, 2% PEG 400, 100mM imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2008 / Details: Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3354 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.22 Å / Num. obs: 13777 / % possible obs: 89.9 % / Redundancy: 13.7 % / Biso Wilson estimate: 23.16 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 1.8→1.94 Å / Redundancy: 5 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1911 / Rsym value: 0.463 / % possible all: 88.2 |
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Processing
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Refinement | Method to determine structure: ![]() Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=LG1 NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=37. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=LG1 NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2314. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=37. NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
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Displacement parameters | Biso mean: 27.68 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→37.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.94 Å / Total num. of bins used: 7
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