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Yorodumi- PDB-5a3i: Crystal Structure of a Complex formed between FLD194 Fab and Tran... -
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-Basic information
Entry | Database: PDB / ID: 5a3i | |||||||||
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Title | Crystal Structure of a Complex formed between FLD194 Fab and Transmissible Mutant H5 Haemagglutinin | |||||||||
Components |
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Keywords | VIRAL PROTEIN / HAEMAGGLUTININ / NEUTRALIZING ANTIBODY / BIRD FLU / H5N1 / INFLUENZA VIRUS / GLYCOPROTEIN | |||||||||
Function / homology | Function and homology information viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / identical protein binding Similarity search - Function | |||||||||
Biological species | INFLUENZA A VIRUS HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å | |||||||||
Authors | Xiong, X. / Corti, D. / Liu, J. / Pinna, D. / Foglierini, M. / Calder, L.J. / Martin, S.R. / Lin, Y.P. / Walker, P.A. / Collins, P.J. ...Xiong, X. / Corti, D. / Liu, J. / Pinna, D. / Foglierini, M. / Calder, L.J. / Martin, S.R. / Lin, Y.P. / Walker, P.A. / Collins, P.J. / Monne, I. / Suguitan Jr, A.L. / Santos, C. / Temperton, N.J. / Subbarao, K. / Lanzavecchia, A. / Gamblin, S.J. / Skehel, J.J. | |||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Structures of Complexes Formed by H5 Influenza Hemagglutinin with a Potent Broadly Neutralizing Human Monoclonal Antibody. Authors: Xiong, X. / Corti, D. / Liu, J. / Pinna, D. / Foglierini, M. / Calder, L.J. / Martin, S.R. / Lin, Y.P. / Walker, P.A. / Collins, P.J. / Monne, I. / Suguitan, A.L.J. / Santos, C. / Temperton, ...Authors: Xiong, X. / Corti, D. / Liu, J. / Pinna, D. / Foglierini, M. / Calder, L.J. / Martin, S.R. / Lin, Y.P. / Walker, P.A. / Collins, P.J. / Monne, I. / Suguitan, A.L.J. / Santos, C. / Temperton, N.J. / Subbarao, K. / Lanzavecchia, A. / Gamblin, S.J. / Skehel, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a3i.cif.gz | 738.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a3i.ent.gz | 614.8 KB | Display | PDB format |
PDBx/mmJSON format | 5a3i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/5a3i ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a3i | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 4 molecules AEBF
#1: Protein | Mass: 37176.121 Da / Num. of mol.: 2 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 17-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/VIETNAM/1203/2004(H5N1)) Variant: TRANSMISSIBLE MUTANT / Plasmid: PACGP67A / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A5A5M5, UniProt: Q6DQ33*PLUS #2: Protein | | Mass: 19097.990 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/VIETNAM/1203/2004(H5N1)) Variant: TRANSMISSIBLE MUTANT / Plasmid: PACGP67A / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A5A5M5, UniProt: A8UDR1*PLUS #5: Protein | | Mass: 19069.977 Da / Num. of mol.: 1 Fragment: HA1 OF TRYPSIN RELEASED ECTODOMAIN, RESIDUES 347-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) INFLUENZA A VIRUS (A/VIETNAM/1203/2004(H5N1)) Variant: TRANSMISSIBLE MUTANT / Plasmid: PACGP67A / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: A5A5M5, UniProt: A8UDR1*PLUS |
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-Antibody , 2 types, 4 molecules CGDH
#3: Antibody | Mass: 24630.686 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) #4: Antibody | Mass: 23830.592 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) |
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-Sugars , 2 types, 3 molecules
#6: Polysaccharide | Source method: isolated from a genetically manipulated source #7: 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS PH 7.5, 10% PEG 4000, 16% ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→83.33 Å / Num. obs: 57328 / % possible obs: 91.4 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.89→2.99 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.9 / % possible all: 78.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 4BH2, 3ZTN Resolution: 2.89→83.33 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.861 / SU B: 43.841 / SU ML: 0.366 / Cross valid method: THROUGHOUT / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES WITH TLS ADDED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.583 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→83.33 Å
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Refine LS restraints |
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