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Yorodumi- PDB-6wwc: Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.0... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wwc | ||||||
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Title | Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with S48K mutation in light chain in complex with HIV fusion peptide (residue 512-519) | ||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / HIV / fusion peptide / antibody / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||
Function / homology | Function and homology information Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / 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 / host cell plasma membrane / structural molecule activity / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.563 Å | ||||||
Authors | Xu, K. / Wang, Y. / Kwong, P.D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: Mutational fitness landscapes reveal genetic and structural improvement pathways for a vaccine-elicited HIV-1 broadly neutralizing antibody. Authors: Madan, B. / Zhang, B. / Xu, K. / Chao, C.W. / O'Dell, S. / Wolfe, J.R. / Chuang, G.Y. / Fahad, A.S. / Geng, H. / Kong, R. / Louder, M.K. / Nguyen, T.D. / Rawi, R. / Schon, A. / Sheng, Z. / ...Authors: Madan, B. / Zhang, B. / Xu, K. / Chao, C.W. / O'Dell, S. / Wolfe, J.R. / Chuang, G.Y. / Fahad, A.S. / Geng, H. / Kong, R. / Louder, M.K. / Nguyen, T.D. / Rawi, R. / Schon, A. / Sheng, Z. / Nimrania, R. / Wang, Y. / Zhou, T. / Lin, B.C. / Doria-Rose, N.A. / Shapiro, L. / Kwong, P.D. / DeKosky, B.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wwc.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wwc.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 6wwc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wwc_validation.pdf.gz | 467.7 KB | Display | wwPDB validaton report |
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Full document | 6wwc_full_validation.pdf.gz | 482 KB | Display | |
Data in XML | 6wwc_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 6wwc_validation.cif.gz | 45.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/6wwc ftp://data.pdbj.org/pub/pdb/validation_reports/ww/6wwc | HTTPS FTP |
-Related structure data
Related structure data | 6wx2C 6cdoS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
#1: Antibody | Mass: 23073.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #2: Antibody | Mass: 24179.842 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human) #3: Protein/peptide | Mass: 732.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS #4: Water | ChemComp-HOH / | |
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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: 2.36 Å3/Da / Density % sol: 47.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-HCl, pH 8.5, 30% v/v PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 23890 / % possible obs: 97.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.083 / Rrim(I) all: 0.15 / Χ2: 0.749 / Net I/σ(I): 5.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6CDO Resolution: 2.563→35.263 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.02 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.71 Å2 / Biso mean: 42.9783 Å2 / Biso min: 22.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.563→35.263 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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