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Yorodumi- PDB-4o58: Crystal structure of broadly neutralizing antibody F045-092 in co... -
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-Basic information
Entry | Database: PDB / ID: 4o58 | |||||||||
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Title | Crystal structure of broadly neutralizing antibody F045-092 in complex with A/Victoria/3/1975 (H3N2) influenza hemagglutinin | |||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / immunoglobulin / virus attachment and entry / immune recognition / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / CD22 mediated BCR regulation / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / positive regulation of B cell activation / phagocytosis, recognition / CD22 mediated BCR regulation / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / phagocytosis, engulfment / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / viral budding from plasma membrane / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / blood microparticle / host cell surface receptor binding / defense response to bacterium / fusion of virus membrane with host plasma membrane / external side of plasma membrane / innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Influenza A virus Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7501 Å | |||||||||
Authors | Lee, P.S. / Wilson, I.A. | |||||||||
Citation | Journal: Nat Commun / Year: 2014 Title: Receptor mimicry by antibody F045-092 facilitates universal binding to the H3 subtype of influenza virus. Authors: Lee, P.S. / Ohshima, N. / Stanfield, R.L. / Yu, W. / Iba, Y. / Okuno, Y. / Kurosawa, Y. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o58.cif.gz | 381.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o58.ent.gz | 311.5 KB | Display | PDB format |
PDBx/mmJSON format | 4o58.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o58_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4o58_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4o58_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 4o58_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/4o58 ftp://data.pdbj.org/pub/pdb/validation_reports/o5/4o58 | HTTPS FTP |
-Related structure data
Related structure data | 4o5iC 4o5lC 4o5nC 4gmsS 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
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 35453.848 Da / Num. of mol.: 1 / Fragment: Hemagglutinin HA1 chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/3/1975 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03435 |
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#2: Protein | Mass: 20225.393 Da / Num. of mol.: 1 / Fragment: Hemagglutinin HA2 chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/3/1975 H3N2 / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P03435 |
-Antibody , 2 types, 2 molecules LH
#3: Antibody | Mass: 22626.895 Da / Num. of mol.: 1 / Fragment: Fab F045-092 light chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IGL@, IGLC2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P0CG05 |
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#4: Antibody | Mass: 25719.725 Da / Num. of mol.: 1 / Fragment: Fab F045-092 heavy chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: S6C4S0 |
-Sugars , 3 types, 5 molecules
#5: Polysaccharide | Source method: isolated from a genetically manipulated source #6: 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 #7: Sugar | |
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-Non-polymers , 3 types, 93 molecules
#8: Chemical | ChemComp-SO4 / #9: Chemical | #10: 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: 4.59 Å3/Da / Density % sol: 73.19 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1 Details: 1.7 M ammonium sulfate, 0.1 M Tris pH 8.1, 4% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03322 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 3, 2013 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03322 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. all: 50811 / Num. obs: 50811 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.75→2.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / Rsym value: 0.71 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4GMS and apo F045-092 structure Resolution: 2.7501→49.022 Å / SU ML: 0.33 / σ(F): 2 / Phase error: 20.33 / 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: 2.7501→49.022 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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