Solution NMR structure of human myeloid differentiation primary response (MyD88). Northeast Structural Genomics target HR2869A
Northeast Structural Genomics Consortium (NESG)
Solution NMR Structure of Human Myeloid Differentiation Primary Response (MyD88).
Myeloid differentiation primary response protein MyD88
MGITTLDDPLGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVS DDYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFITVCDYTNPCTKSWFWTRLAKALSLPLEHHHHHH
Northeast Structural Genomics Consortium
MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR T1/T2. MEASURED TC = 12.1 +/- 1NS AT 20DEG. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA AND AUTOSTRUCTURE IN A CONSENSUS APPROACH. SIMULATED ANNEALING MD LOWEST TARGET FUNCTION SELECTED WITH CYANA, LOWEST ENERGY SELECTED IN AUTOSTRUCTURE USING NIH-XPLOR FOR SIMULATEED ANNEALING MD. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS (EXCLUDING C-TERM TAG): BACKBONE 94.36%, SIDECHAIN 95.8%, AROMATIC (SC) 93.1%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS SIDECHAIN NH2 100%. STRUCTURE BASED ON 2795 NOE. 100 STRUCTURES CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.35 A (1MODEL). 16 CLOSE CONTACTS TOTAL PER 20 MODELS. STRUCTURE QUALITY FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - ALPHA HELIX (28-39, 68-71, 81-85, 87-99, 103-106, 141-150), BETA-STRAND (48-49, 17-22, 72-78, 108-112, 130-131) [S(PHI)+ (PSI)] > 1.8. RMSD 0.6 BB, 0.9 ALL HEAVY ATOMS. RAMACHANDRAN: 88.0% MOST FAV, 11.4% ADDTL ALLOW, 0.5 GENEROUS ALLOW, 0.1% DISALLOW. PROCHECK (PSI-PHI): -0.22/-0.55 (RAW/Z), PROCHECK (ALL): -0.15/-0.89 (RAW/Z), MOLPROBITY CLASH: 27.22/-3.15 (RAW/Z). RPF SCORES ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): RECALL: 0.934, PRECISION: 0.892, F-MEASURE: 0.913, DP-SCORE: 0.721.
0.8 mM [U-5% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 95% H2O/5% D2O
0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 100% D2O
0.8 mM [U-100% 13C; U-100% 15N] protein, 10 mM DTT, 40 mM ammonium acetate, 5 % acetonitrile, 95% H2O/5% D2O
Zimmerman, Moseley, Kulikowski and Montelione
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Th
Brunger, Adams, Clore, Gros, Nilges and Read
Schwieters, Kuszewski, Tjandra and Clore
MYD88_HUMAN, TIR DOMAIN, TOLL LIKE RECEPTOR ADAPTOR DOMAIN, innate immune signaling, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, SIGNALING PROTEIN
GITTLDDPLGHMPERFDAFICYCPSDIQFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSD DYLQSKECDFQTKFALSLSPGAHQKRLIPIKYKAMKKEFPSILRFITVCDYTNPCTKSWFWTRLAKALSLP