+Open data
-Basic information
Entry | Database: PDB / ID: 3mx5 | ||||||
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Title | Lassa fever virus nucleoprotein complexed with UTP | ||||||
Components | Nucleoprotein | ||||||
Keywords | NUCLEAR PROTEIN / Nucleoprotein / Lassa fever virus / Structural Genomics / Scottish Structural Proteomics Facility / SSPF | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / 3'-5' exonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / virus-mediated perturbation of host defense response / RNA binding / identical protein binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lassa virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å | ||||||
Authors | Qi, X. / Lan, S. / Wang, W. / Schelde, L.M. / Dong, H. / Wallat, G. / Liang, Y. / Ly, H. / Dong, C. / Scottish Structural Proteomics Facility (SSPF) | ||||||
Citation | Journal: Nature / Year: 2010 Title: Cap binding and immune evasion revealed by Lassa nucleoprotein structure. Authors: Qi, X. / Lan, S. / Wang, W. / Schelde, L.M. / Dong, H. / Wallat, G.D. / Ly, H. / Liang, Y. / Dong, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mx5.cif.gz | 580.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mx5.ent.gz | 474.9 KB | Display | PDB format |
PDBx/mmJSON format | 3mx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/3mx5 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/3mx5 | HTTPS FTP |
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-Related structure data
Related structure data | 3mwpSC 3mwtC 3mx2C 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 63965.145 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lassa virus / Strain: Mouse/Sierra Leone/Josiah/1976 / Gene: N, Nucleoprotein / Plasmid: pLou3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta / References: UniProt: P13699 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG3350, 0.2 M Lithium chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.903→88.56 Å / Num. all: 79046 / Num. obs: 79030 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.075 / Rsym value: 0.076 / Net I/σ(I): 12.6 | |||||||||||||||
Reflection shell | Resolution: 1.903→1.96 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.49 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3MWP Resolution: 1.903→76.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.225 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.375 Å2
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Refinement step | Cycle: LAST / Resolution: 1.903→76.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.903→1.952 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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