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Yorodumi- PDB-3alx: Crystal structure of the measles virus hemagglutinin bound to its... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3alx | ||||||
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Title | Crystal structure of the measles virus hemagglutinin bound to its cellular receptor SLAM (MV-H(L482R)-SLAM(N102H/R108Y) fusion) | ||||||
Components | Hemagglutinin,LINKER,CDw150 | ||||||
Keywords | Viral Protein/membrane protein / viral protein-receptor complex / six-bladed beta-propeller fold / Immunoglobulin fold / beta-sandwich / Viral Protein-membrane protein complex | ||||||
Function / homology | Function and homology information lymphocyte activation / host cell membrane / positive regulation of type II interferon production / signaling receptor activity / host cell surface receptor binding / symbiont entry into host cell / external side of plasma membrane / viral envelope / virion attachment to host cell / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Measles morbillivirus synthetic construct (others) Saguinus oedipus (cotton-top tamarin) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | ||||||
Authors | Hashiguchi, T. / Ose, T. / Kubota, M. / Maita, N. / Kamishikiryo, J. / Maenaka, K. / Yanagi, Y. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2011 Title: Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM Authors: Hashiguchi, T. / Ose, T. / Kubota, M. / Maita, N. / Kamishikiryo, J. / Maenaka, K. / Yanagi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3alx.cif.gz | 408.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3alx.ent.gz | 331 KB | Display | PDB format |
PDBx/mmJSON format | 3alx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/3alx ftp://data.pdbj.org/pub/pdb/validation_reports/al/3alx | HTTPS FTP |
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-Related structure data
Related structure data | 3alwC 3alzC 2zb6S C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 62122.855 Da / Num. of mol.: 4 Fragment: Hemagglutinin head domain,CD150 V domain, UNP reisudes 30-140 Mutation: L482R(MV-H)/N102H, R108Y(SLAM),L482R(MV-H)/N102H, R108Y(SLAM) Source method: isolated from a genetically manipulated source Details: MV-H/SLAM fusion protein Source: (gene. exp.) Measles morbillivirus, (gene. exp.) synthetic construct (others), (gene. exp.) Saguinus oedipus (cotton-top tamarin) Plasmid: pCA7 / Gene: CDw150 / Cell line (production host): HEK293SGnTI(-) / Production host: Homo sapiens (human) / References: UniProt: E2RZS2, UniProt: Q9GJT3 #2: Sugar | ChemComp-NAG / |
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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: 3.16 Å3/Da / Density % sol: 61.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, floating drop / pH: 8.3 Details: 0.1M imidazole pH8.3, 0.5M (NH4)2SO4, 0.7M Li2SO4, 0.05M Li(AcO)2, 1% ethylene glycol, vapor diffusion, floating drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→50 Å / Num. all: 55721 / Num. obs: 52457 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 3.15→3.26 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5246 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZB6 Resolution: 3.15→19.97 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4656519.52 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.5979 Å2 / ksol: 0.33 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.15→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.35 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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