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Yorodumi- PDB-1a14: COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1a14 | |||||||||
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Title | COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CHAIN ANTIBODY WITH A 5 RESIDUE LINKER AND INFLUENZA VIRUS NEURAMINIDASE | |||||||||
Components |
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Keywords | COMPLEX (ANTIBODY/ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) / SINGLE-CHAIN ANTIBODY / GLYCOSYLATED PROTEIN / COMPLEX (ANTIBODY-ANTIGEN) complex | |||||||||
Function / homology | Function and homology information immunoglobulin production / Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis ...immunoglobulin production / Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / CD22 mediated BCR regulation / Role of LAT2/NTAL/LAB on calcium mobilization / FCERI mediated MAPK activation / Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / FCERI mediated Ca+2 mobilization / FCERI mediated NF-kB activation / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of actin dynamics for phagocytic cup formation / positive regulation of B cell activation / phagocytosis, recognition / immunoglobulin complex / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / phagocytosis, engulfment / exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / immunoglobulin complex, circulating / immunoglobulin receptor binding / viral budding from plasma membrane / complement activation, classical pathway / antigen binding / B cell receptor signaling pathway / adaptive immune response / carbohydrate metabolic process / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / host cell plasma membrane / virion membrane / extracellular space / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Influenza A virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Malby, R.L. / Mccoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Three-dimensional structures of single-chain Fv-neuraminidase complexes. Authors: Malby, R.L. / McCoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M. #1: Journal: Proteins / Year: 1993 Title: Recombinant Antineuraminidase Single Chain Antibody: Expression, Characterization, and Crystallization in Complex with Antigen Authors: Malby, R.L. / Caldwell, J.B. / Gruen, L.C. / Harley, V.R. / Ivancic, N. / Kortt, A.A. / Lilley, G.G. / Power, B.E. / Webster, R.G. / Colman, P.M. / Hudson, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1a14.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1a14.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 1a14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a14_validation.pdf.gz | 517.7 KB | Display | wwPDB validaton report |
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Full document | 1a14_full_validation.pdf.gz | 545.7 KB | Display | |
Data in XML | 1a14_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1a14_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a14 ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a14 | HTTPS FTP |
-Related structure data
Related structure data | 1nmcSC 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
-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 13225.504 Da / Num. of mol.: 1 Fragment: VH DOMAIN OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIVE-RESIDUE POLYPEPTIDE LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094, UniProt: P01749*PLUS |
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#3: Antibody | Mass: 11384.294 Da / Num. of mol.: 1 Fragment: VL DOMAIN OF ANTI-NEURAMINIDASE ANTIBODY NC10 COVALENTLY JOINED BY A FIVE-RESIDUE POLYPEPTIDE LINKER Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: GenBank: 501094, UniProt: P01645*PLUS |
-Protein / Non-polymers , 2 types, 2 molecules N
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 82 - 468 / Source method: isolated from a natural source / Source: (natural) Influenza A virus / Genus: Influenzavirus A / Strain: N9, A/TERN/AUSTRALIA/G70C/75 / References: UniProt: P03472, exo-alpha-sialidase |
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#7: Chemical | ChemComp-CA / |
-Sugars , 3 types, 4 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-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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#5: Sugar | ChemComp-MAN / |
#6: Sugar |
-Details
Nonpolymer details | THE THREE OLIGOSACCHARIDES COVALENTLY ATTACHED TO N9 NEURAMINIDASE ARE NUMBERED BY THE ASN RESIDUE ...THE THREE OLIGOSACCH |
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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 Å3/Da / Density % sol: 70 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 6.6 Details: NC10 SCFV(5) AND N9 NA WERE MIXED TOGETHER (SCFV(5) IN FOUR-FOLD MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOR DIFFUSION ...Details: NC10 SCFV(5) AND N9 NA WERE MIXED TOGETHER (SCFV(5) IN FOUR-FOLD MOLAR EXCESS) WITH AND EQUAL VOLUME OF POTASSIUM PHOSPHATE BUFFER 1.7M PH6.6. THE DROP WAS EQUILIBRATED BY VAPOR DIFFUSION AGAINST PHOSPHATE BUFFER 1.3M PH6.8., vapor diffusion PH range: 6.6-6.8 | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting dropDetails: 1 was mixed with 2 in the molar ration 1:4, and an equal volume of 3 was added. | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 |
Detector | Type: PHOTON FACTORY / Detector: IMAGE PLATE / Date: Jul 1, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.5 Å / Num. obs: 29660 / % possible obs: 68 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.118 |
Reflection shell | Resolution: 2.5→2.6 Å / % possible all: 40 |
Reflection | *PLUS Num. measured all: 86319 |
Reflection shell | *PLUS % possible obs: 40 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NMC Resolution: 2.5→7 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: A POSTERIORI / σ(F): 2
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Refine analyze | Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(I): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |