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Yorodumi- PDB-5vgj: Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Direct... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vgj | |||||||||
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Title | Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing Antibody Isolated from Donor N90, bound to a scaffolded WITO V1V2 domain | |||||||||
Components |
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Keywords | Viral protein/IMMUNE SYSTEM / Fab / HIV-1 / V1V2 / Env / Antibody / Envelope / Neutralizing / IMMUNE SYSTEM / WITO / 1FD6 / Viral protein-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information 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 / 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 ...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 / 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 / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Human immunodeficiency virus 1 Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.456 Å | |||||||||
Authors | Gorman, J. / Li, J. / Kwong, P.D. | |||||||||
Citation | Journal: Immunity / Year: 2017 Title: Virus-like Particles Identify an HIV V1V2 Apex-Binding Neutralizing Antibody that Lacks a Protruding Loop. Authors: Cale, E.M. / Gorman, J. / Radakovich, N.A. / Crooks, E.T. / Osawa, K. / Tong, T. / Li, J. / Nagarajan, R. / Ozorowski, G. / Ambrozak, D.R. / Asokan, M. / Bailer, R.T. / Bennici, A.K. / Chen, ...Authors: Cale, E.M. / Gorman, J. / Radakovich, N.A. / Crooks, E.T. / Osawa, K. / Tong, T. / Li, J. / Nagarajan, R. / Ozorowski, G. / Ambrozak, D.R. / Asokan, M. / Bailer, R.T. / Bennici, A.K. / Chen, X. / Doria-Rose, N.A. / Druz, A. / Feng, Y. / Joyce, M.G. / Louder, M.K. / O'Dell, S. / Oliver, C. / Pancera, M. / Connors, M. / Hope, T.J. / Kepler, T.B. / Wyatt, R.T. / Ward, A.B. / Georgiev, I.S. / Kwong, P.D. / Mascola, J.R. / Binley, J.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vgj.cif.gz | 135.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vgj.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vgj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vgj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5vgj_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5vgj_validation.xml.gz | 23 KB | Display | |
Data in CIF | 5vgj_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/5vgj ftp://data.pdbj.org/pub/pdb/validation_reports/vg/5vgj | HTTPS FTP |
-Related structure data
Related structure data | 5ewiSC S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules G
#1: Protein | Mass: 14761.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Strain: WITO / Cell line (production host): HEK293 GNTI- / Production host: Homo sapiens (human) / References: UniProt: Q5G5U5*PLUS |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25151.197 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 24123.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human) |
-Sugars , 3 types, 4 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 #6: Sugar | ChemComp-NAG / | |
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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: 3.32 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 27% isopropanol, 0.1M imidazole pH 6.5 and 10% PEG8000 were flash-frozen in liquid nitrogen in mother liquor supplemented with 20% 2-methyl-2,4-pentanedial (MPD). |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 13, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.45→50 Å / Num. obs: 10463 / % possible obs: 90.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 106.17 Å2 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.115 / Rrim(I) all: 0.24 / Χ2: 1.016 / Net I/σ(I): 10.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EWI Resolution: 3.456→37.614 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.456→37.614 Å
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Refine LS restraints |
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LS refinement shell |
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