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Yorodumi- PDB-8vqq: Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza vi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vqq | ||||||
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Title | Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with small molecule 6S | ||||||
Components | (Hemagglutinin ...) x 2 | ||||||
Keywords | VIRAL PROTEIN / H1N1 / Hemagglutinin | ||||||
Function / homology | Function and homology information Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation ...Transport of HA trimer, NA tetramer and M2 tetramer from the endoplasmic reticulum to the Golgi Apparatus / Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / Budding / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral mRNA Translation / viral budding from plasma membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Lin, T.H. / Zhu, Y. / Wilson, I.A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Ultrapotent influenza hemagglutinin fusion inhibitors developed through SuFEx-enabled high-throughput medicinal chemistry. Authors: Kitamura, S. / Lin, T.H. / Lee, C.D. / Takamura, A. / Kadam, R.U. / Zhang, D. / Zhu, X. / Dada, L. / Nagai, E. / Yu, W. / Yao, Y. / Sharpless, K.B. / Wilson, I.A. / Wolan, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vqq.cif.gz | 121.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vqq.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8vqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vqq_validation.pdf.gz | 983.5 KB | Display | wwPDB validaton report |
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Full document | 8vqq_full_validation.pdf.gz | 984.5 KB | Display | |
Data in XML | 8vqq_validation.xml.gz | 20.9 KB | Display | |
Data in CIF | 8vqq_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vq/8vqq ftp://data.pdbj.org/pub/pdb/validation_reports/vq/8vqq | HTTPS FTP |
-Related structure data
Related structure data | 8sd2C 8sd4C 8vqlC 8vqmC 8vqnC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
-Hemagglutinin ... , 2 types, 2 molecules AB
#1: Protein | Mass: 36077.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Gene: HA Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: P03452 |
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#2: Protein | Mass: 25106.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus (A/Puerto Rico/8/1934(H1N1)) Gene: HA Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths) References: UniProt: P03452 |
-Sugars , 2 types, 2 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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-NAG / |
-Non-polymers , 2 types, 156 molecules
#4: Chemical | ChemComp-A1ADC / [ Mass: 495.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28ClFN4O3S / Feature type: SUBJECT OF INVESTIGATION |
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#6: Water | ChemComp-HOH / |
-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: 2.78 Å3/Da / Density % sol: 55.7 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Tris, 1M Lithium Chloride, 20% PEG6000, PH8 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 19, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→42.7 Å / Num. obs: 37695 / % possible obs: 90 % / Redundancy: 22.5 % / CC1/2: 1 / Rpim(I) all: 0.05 / Rrim(I) all: 0.24 / Net I/σ(I): 26.9 |
Reflection shell | Resolution: 2.05→2.13 Å / Num. unique obs: 37641 / CC1/2: 0.3 / Rpim(I) all: 0.74 / Rrim(I) all: 2.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→42.7 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.84 / 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: 2.05→42.7 Å
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Refine LS restraints |
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LS refinement shell |
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