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Yorodumi- PDB-5a3i: Crystal Structure of a Complex formed between FLD194 Fab and Tran... -
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Open data
- Basic information
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 / host cell surface receptor binding / 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 / membrane 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 visualization
| Structure viewer | Molecule:  Molmil  Jmol/JSmol | 
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- Downloads & links
Downloads & links
- Download
Download
| PDBx/mmCIF format |  5a3i.cif.gz | 738.9 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
| Summary document |  5a3i_validation.pdf.gz | 1.1 MB | Display |  wwPDB validaton report | 
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| Full document |  5a3i_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML |  5a3i_validation.xml.gz | 59.8 KB | Display | |
| Data in CIF |  5a3i_validation.cif.gz | 81.5 KB | Display | |
| Arichive directory |  https://data.pdbj.org/pub/pdb/validation_reports/a3/5a3i  ftp://data.pdbj.org/pub/pdb/validation_reports/a3/5a3i | HTTPS FTP | 
-Related structure data
- Links
Links
- Assembly
Assembly
| Deposited unit |  
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| 1 |  
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| 2 |  
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| Unit cell | 
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- Components
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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-Details
| Has protein modification | Y | 
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-Experimental details
-Experiment
| Experiment | Method:  X-RAY DIFFRACTION / Number of used crystals: 1 | 
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- Sample preparation
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
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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