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- PDB-5vob: Crystal structure of HCMV Pentamer in complex with neutralizing a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vob | |||||||||
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Title | Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 | |||||||||
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![]() | Viral Protein/Immune System / HCMV / neutralizing epitope / immunogen / viral entry / Pentamer / vaccine / Viral Protein-Immune System complex | |||||||||
Function / homology | ![]() immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / host cell endosome membrane / HCMV Late Events / antigen binding / HCMV Early Events / antibacterial humoral response / host cell Golgi apparatus / blood microparticle ...immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / host cell endosome membrane / HCMV Late Events / antigen binding / HCMV Early Events / antibacterial humoral response / host cell Golgi apparatus / blood microparticle / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / immune response / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Malito, E. / Chandramouli, S. | |||||||||
![]() | ![]() Title: Structural basis for potent antibody-mediated neutralization of human cytomegalovirus. Authors: Chandramouli, S. / Malito, E. / Nguyen, T. / Luisi, K. / Donnarumma, D. / Xing, Y. / Norais, N. / Yu, D. / Carfi, 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 | ![]() | 366.9 KB | Display | ![]() |
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PDB format | ![]() | 292.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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
-Envelope glycoprotein ... , 5 types, 5 molecules ABCDE
#1: Protein | Mass: 82415.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 30846.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Protein | Mass: 19777.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Protein | Mass: 28664.604 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#5: Protein | Mass: 15011.043 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Antibody , 2 types, 2 molecules HL
#6: Antibody | Mass: 30873.584 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#7: Antibody | Mass: 25714.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Sugars , 2 types, 11 molecules ![](data/chem/img/NAG.gif)
#8: 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 |
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#9: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 10% (wt/vol) PEG400 10% isopropanol 2% (wt/vol) benzamidine 0.1M Tris pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.4 Å / Num. obs: 62201 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 103.93 Å2 / CC1/2: 0.995 / Rsym value: 0.277 / Net I/σ(I): 8.87 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 11.8 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 72320 / CC1/2: 0.362 / Rsym value: 3.28 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 94.01 Å2
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Refine analyze | Luzzati coordinate error obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.02→49.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.02→3.1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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