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- PDB-5w5u: Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza vi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w5u | |||||||||
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Title | Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141037 (P4) | |||||||||
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![]() | VIRAL PROTEIN / Glycoprotein / Ectodomain / N-glycosylation | |||||||||
Function / homology | ![]() 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 | ![]() ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wilson, I.A. / Kadam, R.U. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Potent peptidic fusion inhibitors of influenza virus. Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Buyck, C. / Schepens, W.B.G. / Kesteleyn, B. / Stoops, B. / Vreeken, R.J. / Vermond, J. / Goutier, W. / Tang, C. / Vogels, R. / Friesen, R.H.E. ...Authors: Kadam, R.U. / Juraszek, J. / Brandenburg, B. / Buyck, C. / Schepens, W.B.G. / Kesteleyn, B. / Stoops, B. / Vreeken, R.J. / Vermond, J. / Goutier, W. / Tang, C. / Vogels, R. / Friesen, R.H.E. / Goudsmit, J. / van Dongen, M.J.P. / Wilson, I.A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 224.5 KB | Display | ![]() |
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PDB format | ![]() | 177.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.8 KB | Display | ![]() |
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Full document | ![]() | 788.9 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w5sC ![]() 5w6iC ![]() 5w6rC ![]() 5w6tC ![]() 5w6uC ![]() 1ru7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 36650.293 Da / Num. of mol.: 1 / Fragment: residues 18-343 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: ![]() |
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#2: Protein | Mass: 20138.393 Da / Num. of mol.: 1 / Fragment: residues 344-519 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: A/Puerto Rico/8/1934 H1N1 / Gene: HA / Production host: ![]() |
-Protein/peptide , 1 types, 1 molecules D
#3: Protein/peptide | Mass: 1486.708 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Sugars , 2 types, 5 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | 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, 59 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: HA conc. 11 mg/ml 1M lithium chloride 10% w/v PEG 6000 0.1M sodium citrate, pH= 5.0 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→50 Å / Num. obs: 25055 / % possible obs: 98.4 % / Redundancy: 4.4 % / CC1/2: 0.93 / Rpim(I) all: 0.04 / Rsym value: 0.08 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.46→2.5 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1249 / CC1/2: 0.65 / Rpim(I) all: 0.44 / Rsym value: 0.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1RU7 Resolution: 2.461→31.646 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.34
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.461→31.646 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -21.091 Å / Origin y: -35.4558 Å / Origin z: -9.9274 Å
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Refinement TLS group | Selection details: all |