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Yorodumi- PDB-3alw: Crystal structure of the measles virus hemagglutinin bound to its... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3alw | ||||||
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Title | Crystal structure of the measles virus hemagglutinin bound to its cellular receptor SLAM (Form I, MV-H-SLAM(N102H/R108Y) fusion) | ||||||
Components | Hemagglutinin, 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 / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / external side of plasma membrane / viral envelope / virion attachment to host cell ...lymphocyte activation / host cell membrane / positive regulation of type II interferon production / signaling receptor activity / receptor ligand activity / host cell surface receptor binding / symbiont entry into host cell / external side of plasma membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Measles virus synthetic construct (others) Saguinus oedipus (cotton-top tamarin) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 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 | 3alw.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3alw.ent.gz | 88.9 KB | Display | PDB format |
PDBx/mmJSON format | 3alw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3alw_validation.pdf.gz | 459.5 KB | Display | wwPDB validaton report |
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Full document | 3alw_full_validation.pdf.gz | 492.5 KB | Display | |
Data in XML | 3alw_validation.xml.gz | 24.1 KB | Display | |
Data in CIF | 3alw_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/3alw ftp://data.pdbj.org/pub/pdb/validation_reports/al/3alw | HTTPS FTP |
-Related structure data
Related structure data | 3alxC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 62078.816 Da / Num. of mol.: 1 Fragment: Hemagglutinin head domain/CD150 V domain, UNP reisudes 30-140 Mutation: N692H, R698Y (CDw150) Source method: isolated from a genetically manipulated source Details: MV-H/SLAM fusion protein Source: (gene. exp.) Measles virus, (gene. exp.) synthetic construct (others), (gene. exp.) Saguinus oedipus (cotton-top tamarin) Strain: Edmonston B, B95a / Gene: Hemagglutinin, CD150 / Plasmid: pCA7 / Cell line (production host): HEK293SGnTI(-) / Production host: Homo sapiens (human) References: UniProt: E2RZS2, UniProt: Q9GJT3, UniProt: P08362*PLUS | ||
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#2: Sugar | Sequence details | THE GGGSGGGSGG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 9.990449 Å3/Da / Density % sol: 87.68824 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, floating drop / pH: 5.8 Details: 0.1M imidazole pH5.8, 0.5M (NH4)2SO4, 0.7M Li2SO4, 3% ethylene glycol, VAPOR DIFFUSION, FLOATING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.55→30 Å / Num. obs: 28716 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20 % / Biso Wilson estimate: 78.3 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 38.6 |
Reflection shell | Resolution: 3.55→3.68 Å / Redundancy: 20 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 6.5 / Num. unique all: 2831 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZB6 Resolution: 3.55→29.89 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4911388.71 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 99.3884 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 138.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.55→29.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.55→3.68 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
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Xplor file |
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