HEADER SIGNALING PROTEIN 29-JUN-07 2JS7 TITLE SOLUTION NMR STRUCTURE OF HUMAN MYELOID DIFFERENTIATION PRIMARY TITLE 2 RESPONSE (MYD88). NORTHEAST STRUCTURAL GENOMICS TARGET HR2869A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD88; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL TIR DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MYD88; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: HR2869-NC5J; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21 KEYWDS MYD88_HUMAN, TIR DOMAIN, TOLL LIKE RECEPTOR ADAPTOR DOMAIN, INNATE KEYWDS 2 IMMUNE SIGNALING, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE KEYWDS 3 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 4 SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.ROSSI,T.A.RAMELOT,X.TAO,M.CIANO,C.HO,L.-C.MA,R.XIAO,T.B.ACTON, AUTHOR 2 M.A.KENNEDY,L.TONG,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 6 30-OCT-24 2JS7 1 REMARK REVDAT 5 19-FEB-20 2JS7 1 REMARK SEQADV REVDAT 4 24-JAN-18 2JS7 1 AUTHOR REVDAT 3 27-JUN-12 2JS7 1 AUTHOR VERSN REVDAT 2 24-FEB-09 2JS7 1 VERSN REVDAT 1 23-OCT-07 2JS7 0 JRNL AUTH P.ROSSI,R.XIAO,X.TAO,T.B.ACTON,L.TONG,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF HUMAN MYELOID DIFFERENTIATION JRNL TITL 2 PRIMARY RESPONSE (MYD88). JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, CNS 1.1, X-PLOR NIH 2.11.2 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ (CNS), REMARK 3 SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY REMARK 3 NMR T1/T2. MEASURED TC = 12.1 +/- 1NS AT 20DEG. STRUCTURE REMARK 3 DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS REMARK 3 BY CYANA AND AUTOSTRUCTURE IN A CONSENSUS APPROACH. SIMULATED REMARK 3 ANNEALING MD LOWEST TARGET FUNCTION SELECTED WITH CYANA, LOWEST REMARK 3 ENERGY SELECTED IN AUTOSTRUCTURE USING NIH-XPLOR FOR SIMULATEED REMARK 3 ANNEALING MD. SELECTED MODELS ARE FURTHER REFINED USING CNS IN REMARK 3 EXPLICIT WATER SHELL (NIELGES PROTOCOL WITH PARAM19). ASSIGNMENT REMARK 3 STATS (EXCLUDING C-TERM TAG): BACKBONE 94.36%, SIDECHAIN 95.8%, REMARK 3 AROMATIC (SC) 93.1%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOUS REMARK 3 SIDECHAIN NH2 100%. STRUCTURE BASED ON 2795 NOE. 100 STRUCTURES REMARK 3 CALCULATED 20 LOWEST ENERGY SUBMITTED. MAX NOE VIOLATION 0.35 A REMARK 3 (1MODEL). 16 CLOSE CONTACTS TOTAL PER 20 MODELS. STRUCTURE QUALITY REMARK 3 FACTOR (PSVS 1.3): ORDERED RESIDUES RANGES - ALPHA HELIX (28-39, REMARK 3 68-71, 81-85, 87-99, 103-106, 141-150), BETA-STRAND (48-49, 17-22, REMARK 3 72-78, 108-112, 130-131) [S(PHI)+ REMARK 3 (PSI)] > 1.8. RMSD 0.6 BB, 0.9 ALL HEAVY ATOMS. RAMACHANDRAN: 88.0% REMARK 3 MOST FAV, 11.4% ADDTL ALLOW, 0.5 GENEROUS ALLOW, 0.1% DISALLOW. REMARK 3 PROCHECK (PSI-PHI): -0.22/-0.55 (RAW/Z), PROCHECK (ALL): -0.15/- REMARK 3 0.89 (RAW/Z), MOLPROBITY CLASH: 27.22/-3.15 (RAW/Z). RPF SCORES REMARK 3 ALL ASSIGNED RESIDUES (FIT OF NOESY PEAKLISTS TO STRUCTURE): REMARK 3 RECALL: 0.934, PRECISION: 0.892, F-MEASURE: 0.913, DP-SCORE: 0.721. REMARK 4 REMARK 4 2JS7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100223. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-5% 13C; U-100% 15N] REMARK 210 PROTEIN, 10 MM DTT, 40 MM REMARK 210 AMMONIUM ACETATE, 5 % REMARK 210 ACETONITRILE, 95% H2O/5% D2O; REMARK 210 0.8 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 10 MM DTT, 40 MM REMARK 210 AMMONIUM ACETATE, 5 % REMARK 210 ACETONITRILE, 100% D2O; 0.8 MM REMARK 210 [U-100% 13C; U-100% 15N] PROTEIN, REMARK 210 10 MM DTT, 40 MM AMMONIUM REMARK 210 ACETATE, 5 % ACETONITRILE, 95% REMARK 210 H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D HNCO; 3D HN(COCA) REMARK 210 CB; 3D HN(CO)CA; 3D HN(CA)CO; 3D REMARK 210 HBHA(CO)NH; 3D 1H-13C NOESY; 3D REMARK 210 1H-15N NOESY; 3D HCCH-COSY; 3D REMARK 210 HCCH-TOCSY; 3D CCH-TOCSY; 2D 1H- REMARK 210 13C HSQC STEREOSPECIFIC VL; H/D REMARK 210 EXCH; HETNOE; T1/T2 REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AUTOSTRUCTURE 2.1.1, AUTOASSIGN REMARK 210 1.14, SPARKY 2.110, NMRPIPE 2005, REMARK 210 TOPSPIN 1.3, MOLMOL 2K.2, PSVS REMARK 210 1.3, PROCHECKNMR, MOLPROBITY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LEU A 6 -6.81 83.27 REMARK 500 1 ASP A 8 72.24 -163.83 REMARK 500 1 HIS A 12 96.74 56.46 REMARK 500 1 ARG A 16 -166.10 64.48 REMARK 500 1 THR A 41 78.62 -153.70 REMARK 500 1 ARG A 44 119.48 72.17 REMARK 500 1 VAL A 54 -152.43 -101.59 REMARK 500 1 LEU A 55 143.47 77.54 REMARK 500 1 THR A 58 106.46 52.16 REMARK 500 1 CYS A 59 79.11 -69.63 REMARK 500 1 LEU A 99 -81.55 -76.28 REMARK 500 1 SER A 100 145.14 177.29 REMARK 500 1 LEU A 124 -44.54 -140.96 REMARK 500 1 ARG A 125 49.09 26.64 REMARK 500 1 PHE A 126 83.04 49.10 REMARK 500 1 SER A 139 -72.35 -132.15 REMARK 500 1 PRO A 152 99.91 -61.46 REMARK 500 1 LEU A 153 -84.90 47.61 REMARK 500 1 GLU A 154 42.91 -155.34 REMARK 500 1 HIS A 156 84.26 -68.03 REMARK 500 1 HIS A 158 83.57 -66.08 REMARK 500 1 HIS A 159 -75.67 64.70 REMARK 500 2 MET A 13 129.13 53.51 REMARK 500 2 GLU A 15 32.14 -89.63 REMARK 500 2 GLU A 39 4.07 -69.24 REMARK 500 2 THR A 41 18.61 -153.13 REMARK 500 2 ARG A 44 98.94 68.30 REMARK 500 2 LEU A 99 -90.08 -83.56 REMARK 500 2 SER A 100 149.53 -174.88 REMARK 500 2 LYS A 114 -164.26 -126.38 REMARK 500 2 LEU A 124 -43.70 -138.19 REMARK 500 2 ARG A 125 45.22 31.32 REMARK 500 2 THR A 128 82.99 -157.30 REMARK 500 2 PRO A 152 -92.85 -66.88 REMARK 500 2 LEU A 153 -43.11 -145.05 REMARK 500 2 GLU A 154 -162.68 -105.84 REMARK 500 2 HIS A 156 93.97 -56.16 REMARK 500 2 HIS A 158 55.54 -176.76 REMARK 500 2 HIS A 159 22.28 49.81 REMARK 500 3 THR A 5 106.03 64.08 REMARK 500 3 GLU A 15 84.64 56.43 REMARK 500 3 ARG A 44 36.56 -151.06 REMARK 500 3 PRO A 56 41.98 -73.40 REMARK 500 3 ARG A 73 -72.71 -78.47 REMARK 500 3 LEU A 99 -71.26 -74.77 REMARK 500 3 ARG A 125 48.71 29.59 REMARK 500 4 LEU A 10 -73.52 -109.50 REMARK 500 4 MET A 13 60.53 39.84 REMARK 500 4 THR A 41 -31.86 -154.53 REMARK 500 4 TYR A 43 -85.59 58.53 REMARK 500 REMARK 500 THIS ENTRY HAS 300 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HR2869A RELATED DB: TARGETDB REMARK 900 RELATED ID: 15356 RELATED DB: BMRB DBREF 2JS7 A 2 152 UNP Q99836 MYD88_HUMAN 146 296 SEQADV 2JS7 MET A 1 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 LEU A 153 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 GLU A 154 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 HIS A 155 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 HIS A 156 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 HIS A 157 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 HIS A 158 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 HIS A 159 UNP Q99836 EXPRESSION TAG SEQADV 2JS7 HIS A 160 UNP Q99836 EXPRESSION TAG SEQRES 1 A 160 MET GLY ILE THR THR LEU ASP ASP PRO LEU GLY HIS MET SEQRES 2 A 160 PRO GLU ARG PHE ASP ALA PHE ILE CYS TYR CYS PRO SER SEQRES 3 A 160 ASP ILE GLN PHE VAL GLN GLU MET ILE ARG GLN LEU GLU SEQRES 4 A 160 GLN THR ASN TYR ARG LEU LYS LEU CYS VAL SER ASP ARG SEQRES 5 A 160 ASP VAL LEU PRO GLY THR CYS VAL TRP SER ILE ALA SER SEQRES 6 A 160 GLU LEU ILE GLU LYS ARG CYS ARG ARG MET VAL VAL VAL SEQRES 7 A 160 VAL SER ASP ASP TYR LEU GLN SER LYS GLU CYS ASP PHE SEQRES 8 A 160 GLN THR LYS PHE ALA LEU SER LEU SER PRO GLY ALA HIS SEQRES 9 A 160 GLN LYS ARG LEU ILE PRO ILE LYS TYR LYS ALA MET LYS SEQRES 10 A 160 LYS GLU PHE PRO SER ILE LEU ARG PHE ILE THR VAL CYS SEQRES 11 A 160 ASP TYR THR ASN PRO CYS THR LYS SER TRP PHE TRP THR SEQRES 12 A 160 ARG LEU ALA LYS ALA LEU SER LEU PRO LEU GLU HIS HIS SEQRES 13 A 160 HIS HIS HIS HIS HELIX 1 1 CYS A 24 SER A 26 5 3 HELIX 2 2 ASP A 27 GLN A 40 1 14 HELIX 3 3 ALA A 64 GLU A 66 5 3 HELIX 4 4 LEU A 67 ARG A 71 1 5 HELIX 5 5 SER A 80 SER A 86 1 7 HELIX 6 6 SER A 86 SER A 100 1 15 HELIX 7 7 GLY A 102 ARG A 107 1 6 HELIX 8 8 TRP A 140 LEU A 151 1 12 SHEET 1 A 5 CYS A 48 VAL A 49 0 SHEET 2 A 5 PHE A 17 CYS A 22 1 N ILE A 21 O CYS A 48 SHEET 3 A 5 CYS A 72 VAL A 78 1 O ARG A 74 N PHE A 20 SHEET 4 A 5 LEU A 108 LYS A 112 1 O ILE A 111 N VAL A 77 SHEET 5 A 5 CYS A 130 ASP A 131 1 O CYS A 130 N LYS A 112 SSBOND 1 CYS A 48 CYS A 72 1555 1555 2.90 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1