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Yorodumi- PDB-6q1z: Crystal structure of human 1G04 Fab in complex with influenza vir... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q1z | |||||||||
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Title | Crystal structure of human 1G04 Fab in complex with influenza virus neuraminidase from A/Hunan/02650/2016 (H7N9) | |||||||||
Components |
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Keywords | VIRAL PROTEIN / HYDROLASE/IMMUNE SYSTEM / broadly protective human antibody / neuraminidase / inhibition / active site / antibody-neuraminidase complex / HYDROLASE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / viral budding from plasma membrane / membrane => GO:0016020 / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Influenza A virus Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.446 Å | |||||||||
Authors | Zhu, X. / Wilson, I.A. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2019 Title: Broadly protective human antibodies that target the active site of influenza virus neuraminidase. Authors: Stadlbauer, D. / Zhu, X. / McMahon, M. / Turner, J.S. / Wohlbold, T.J. / Schmitz, A.J. / Strohmeier, S. / Yu, W. / Nachbagauer, R. / Mudd, P.A. / Wilson, I.A. / Ellebedy, A.H. / Krammer, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q1z.cif.gz | 342.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q1z.ent.gz | 274.9 KB | Display | PDB format |
PDBx/mmJSON format | 6q1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q1z_validation.pdf.gz | 629.3 KB | Display | wwPDB validaton report |
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Full document | 6q1z_full_validation.pdf.gz | 637.2 KB | Display | |
Data in XML | 6q1z_validation.xml.gz | 3.6 KB | Display | |
Data in CIF | 6q1z_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/6q1z ftp://data.pdbj.org/pub/pdb/validation_reports/q1/6q1z | HTTPS FTP |
-Related structure data
Related structure data | 6q20C 6q23C 4fqlS 5itbS 5l14S 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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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules LCHD
#2: Antibody | Mass: 23564.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 26109.111 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster) |
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-Protein / Non-polymers , 2 types, 4 molecules AB
#1: Protein | Mass: 43982.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Gene: NA / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A5A4LHS4*PLUS, exo-alpha-sialidase #7: Chemical | |
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-Sugars , 3 types, 6 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | #6: Sugar | |
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-Details
Has ligand of interest | Y |
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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: 3.28 Å3/Da / Density % sol: 62.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES, pH 7.5, 5%(w/v) PEG3000, 30% (w/v) PEG400, 10%(v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03309 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03309 Å / Relative weight: 1 |
Reflection | Resolution: 3.446→47.4 Å / Num. obs: 30994 / % possible obs: 99.1 % / Redundancy: 4.4 % / Biso Wilson estimate: 126 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.05 / Rsym value: 0.09 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 3.45→3.51 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 1539 / CC1/2: 0.844 / Rpim(I) all: 0.48 / Rsym value: 0.87 / % possible all: 0.87 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5L14, 5ITB, 4FQL Resolution: 3.446→47.365 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 27.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.446→47.365 Å
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Refine LS restraints |
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LS refinement shell |
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