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Yorodumi- PDB-2kkz: Solution NMR structure of the monomeric W187R mutant of A/Udorn N... -
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-Basic information
Entry | Database: PDB / ID: 2kkz | ||||||
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Title | Solution NMR structure of the monomeric W187R mutant of A/Udorn NS1 effector domain. Northeast Structural Genomics target OR8C[W187R]. | ||||||
Components | Non-structural protein NS1 | ||||||
Keywords | ANTIVIRAL PROTEIN / Influenza A / Effector Domain / solution NMR structure / W187R mutant / Cytoplasm / Host-virus interaction / Interferon antiviral system evasion / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response ...symbiont-mediated suppression of host cytokine production / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host mRNA processing / symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / double-stranded RNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / host cell nucleus / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Aramini, J.M. / Ma, L. / Lee, H. / Zhao, L. / Cunningham, K. / Ciccosanti, C. / Janjua, H. / Fang, Y. / Xiao, R. / Krug, R.M. ...Aramini, J.M. / Ma, L. / Lee, H. / Zhao, L. / Cunningham, K. / Ciccosanti, C. / Janjua, H. / Fang, Y. / Xiao, R. / Krug, R.M. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Solution NMR structure of the monomeric W187R mutant of A/Udorn NS1 effector domain. Northeast Structural Genomics target OR8C[W187R]. Authors: Aramini, J.M. / Ma, L. / Lee, H. / Zhao, L. / Cunningham, K. / Ciccosanti, C. / Janjua, H. / Fang, Y. / Xiao, R. / Krug, R.M. / Montelione, G.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kkz.cif.gz | 829 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kkz.ent.gz | 695.8 KB | Display | PDB format |
PDBx/mmJSON format | 2kkz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kkz_validation.pdf.gz | 340.8 KB | Display | wwPDB validaton report |
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Full document | 2kkz_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 2kkz_validation.xml.gz | 37 KB | Display | |
Data in CIF | 2kkz_validation.cif.gz | 66.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/2kkz ftp://data.pdbj.org/pub/pdb/validation_reports/kk/2kkz | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15935.354 Da / Num. of mol.: 1 / Fragment: sequence database residues 85-215 / Mutation: W187R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: Udorn/1972 / Gene: NS, NS1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q6XSU2, UniProt: P03495*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED ...Text: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. AUTOMATED BACKBONE ASSIGNMENTS WERE MADE USING AUTOASSIGN, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSplus. ROTAMER STATES OF SPECIFIC ORDERED RESIDUES WERE CONSTRAINED IN THE FINAL STAGE OF THE STRUCTURE REFINEMENT BASED ON PROCHECK. COMPLETENESS OF NMR ASSIGNMENTS (EXCLUDING C-TERMINAL HHHHHH): BACKBONE, 98.3%, SIDE CHAIN, 95.9%, AROMATICS, 97.8%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC SIDE CHAIN NH2: 80%. FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUES 84 TO 217, PSVS 1.3), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] COMPRISE: 87-163,169-202: (A) RMSD (ORDERED RESIDUES): BB, 0.5, HEAVY ATOM, 0.9. (B) RAMACHANDRAN STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 88.4%, ADDITIONALLY ALLOWED, 11.6%, GENEROUSLY ALLOWED, 0.0%, DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.43/-1.38, ALL, -0.30/-1.77. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 17.12/-1.41 (E) RPF SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 84-217): RECALL, 0.968, PRECISION, 0.911, F-MEASURE, 0.939, DP-SCORE, 0.740. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 13. (G) AGREEMENT WITH RESIDUAL DIPOLAR COUPLINGS (20 MODELS): CORRELATION COEFFICIENT (R): 0.992 (0.001); Q RMS: 0.125 (0.008). THE C-TERMINAL HIS TAG RESIDUES OF THE PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < 1.8]: 84-86,164-168,203-END. |
-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 0.1 / pH: 6.9 / Pressure: ambient / Temperature: 300 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2251 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 203 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.5 ...Details: THE FINAL STRUCTURES ARE BASED ON A TOTAL OF 2251 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE CONSTRAINTS AND 203 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND CONSTRAINTS (18.5 CONSTRAINTS PER RESIDUE, 5.5 LONG RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 84 TO 217 BY PSVS 1.3). IN ADDITION, 75 RESOLVED N-H RESIDUAL DIPOLAR COUPLINGS FOR ORDERED RESIDUES WERE INCLUDED IN ALL STRUCTURE CALCULATIONS. STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH PARAM19 AND USING A NEUTRAL HISTIDINE TAUTOMER (ND1H FORM) AT RESIDUE 169. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 5.3 ° / Maximum upper distance constraint violation: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.01 Å |