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Yorodumi- PDB-4r8w: Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4r8w | ||||||
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Title | Crystal structure of H7 hemagglutinin from A/Anhui/1/2013 in complex with a neutralizing antibody CT149 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Influenza A Virus / Hemagglutinin / neutralizing antibody | ||||||
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 / virion membrane Similarity search - Function | ||||||
Biological species | Influenza A virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å | ||||||
Authors | Wu, Y. / Shi, Y. / Qi, J. / Gao, G.F. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: A potent broad-spectrum protective human monoclonal antibody crosslinking two haemagglutinin monomers of influenza A virus Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. ...Authors: Wu, Y. / Cho, M. / Shore, D. / Song, M. / Choi, J. / Jiang, T. / Deng, Y.Q. / Bourgeois, M. / Almli, L. / Yang, H. / Chen, L.M. / Shi, Y. / Qi, J. / Li, A. / Yi, K.S. / Chang, M. / Bae, J.S. / Lee, H. / Shin, J. / Stevens, J. / Hong, S. / Qin, C.F. / Gao, G.F. / Chang, S.J. / Donis, R.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4r8w.cif.gz | 299.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4r8w.ent.gz | 241.6 KB | Display | PDB format |
PDBx/mmJSON format | 4r8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4r8w_validation.pdf.gz | 480.2 KB | Display | wwPDB validaton report |
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Full document | 4r8w_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 4r8w_validation.xml.gz | 27 KB | Display | |
Data in CIF | 4r8w_validation.cif.gz | 36.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/4r8w ftp://data.pdbj.org/pub/pdb/validation_reports/r8/4r8w | HTTPS FTP |
-Related structure data
Related structure data | 4ubdC 4dn3S 4kolS 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 on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 34993.559 Da / Num. of mol.: 1 / Fragment: UNP residues 19-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Anhui/1-BALF_RG45/2013(H7N9)) Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024E3P0 |
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#2: Protein | Mass: 20442.463 Da / Num. of mol.: 1 / Fragment: UNP residues 340-516 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Anhui/1-BALF_RG45/2013(H7N9)) Gene: HA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A024E3P0, UniProt: A0A024E2M1*PLUS |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 24429.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
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#4: Antibody | Mass: 23761.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm) |
-Sugars / Non-polymers , 2 types, 28 molecules
#5: Sugar | #6: 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: 3.06 Å3/Da / Density % sol: 59.81 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: 30% v/v PEG 4000, 60mM Divalents, pH 8.5, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 13, 2013 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.795→50 Å / Num. all: 31761 / Num. obs: 31761 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 66.4 Å2 |
Reflection shell | Resolution: 2.795→2.9 Å / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 4KOL and 4DN3 Resolution: 2.795→48.405 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 33.46 / 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: 2.795→48.405 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: 55.7892 Å / Origin y: -16.1559 Å / Origin z: -21.1885 Å
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Refinement TLS group | Selection details: all |