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- PDB-1a14: COMPLEX BETWEEN NC10 ANTI-INFLUENZA VIRUS NEURAMINIDASE SINGLE CH... -
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Open data
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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 | |||||||||
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![]() | COMPLEX (ANTIBODY/ANTIGEN) / COMPLEX (ANTIBODY-ANTIGEN) / SINGLE-CHAIN ANTIBODY / GLYCOSYLATED PROTEIN / COMPLEX (ANTIBODY-ANTIGEN) complex | |||||||||
Function / homology | ![]() 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 | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Malby, R.L. / Mccoy, A.J. / Kortt, A.A. / Hudson, P.J. / Colman, P.M. | |||||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137.7 KB | Display | ![]() |
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PDB format | ![]() | 109.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 517.7 KB | Display | ![]() |
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Full document | ![]() | 545.7 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nmcSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() ![]() |
-Protein / Non-polymers , 2 types, 2 molecules N![](data/chem/img/CA.gif)
![](data/chem/img/CA.gif)
#1: Protein | Mass: 43723.770 Da / Num. of mol.: 1 / Fragment: RESIDUES 82 - 468 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#7: Chemical | ChemComp-CA / |
-Sugars , 3 types, 4 molecules ![](data/chem/img/MAN.gif)
![](data/chem/img/NAG.gif)
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#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: ![]() |
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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: ![]() ![]() ![]() |
Detector | Type: ![]() ![]() |
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 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(I): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |