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- PDB-4c53: Crystal Structure of Guanarito virus GP2 in the post-fusion confo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c53 | |||||||||
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Title | Crystal Structure of Guanarito virus GP2 in the post-fusion conformation | |||||||||
![]() | PRE-GLYCOPROTEIN POLYPROTEIN GP COMPLEX | |||||||||
![]() | VIRAL PROTEIN / ARENAVIRUS / VENEZUELAN HEMORRHAGIC FEVER / GLYCOPROTEIN / FUSION GLYCOPROTEIN | |||||||||
Function / homology | ![]() host cell Golgi membrane / membrane => GO:0016020 / 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 / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Parsy, M. / Huiskonen, J.T. / Harlos, K. / Bowden, T.A. | |||||||||
![]() | ![]() Title: Crystal Structure of Venezuelan Hemorrhagic Fever Virus Fusion Glycoprotein Reveals a Class 1 Post-Fusion Architecture with Extensive Glycosylation. Authors: Parsy, M. / Harlos, K. / Huiskonen, J.T. / Bowden, T.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 | ![]() | 89.3 KB | Display | ![]() |
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PDB format | ![]() | 69.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 10.8 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mkoS S: Starting model for refinement |
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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: 16285.385 Da / Num. of mol.: 3 / Fragment: ECTODOMAIN, RESIDUES 292-418 Source method: isolated from a genetically manipulated source Details: N-LINKED GLYCOSYLATION SEQUONS AT ASN314, ASN351, ASN359, ASN376, AND ASN381 Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.9 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | pH: 3.5 Details: 0.15 M LI2SO4, 0.1 M CITRIC ACID PH 3.5, 18% W/V PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2013 / Details: MIRRORS |
Radiation | Monochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 4.14→50 Å / Num. obs: 5894 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Biso Wilson estimate: 171.92 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 4.14→4.14 Å / Redundancy: 5.1 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3MKO Resolution: 4.14→38.44 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.9076 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.795
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Displacement parameters | Biso mean: 222.84 Å2
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Refine analyze | Luzzati coordinate error obs: 1.869 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.14→38.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 4.14→4.63 Å / Total num. of bins used: 5
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