HEADER IMMUNE SYSTEM 19-JUL-07 2Z5V TITLE SOLUTION STRUCTURE OF THE TIR DOMAIN OF HUMAN MYD88 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD88; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MYD88 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: BL-21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-5X-3 KEYWDS SIGNAL TRANSDUCTION INNATE IMMUNITY, CYTOPLASM, IMMUNE RESPONSE, KEYWDS 2 INFLAMMATORY RESPONSE, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.OHNISHI,H.TOCHIO,H.HIROAKI,N.KONDO,Z.KATO,M.SHIRAKAWA REVDAT 4 16-MAR-22 2Z5V 1 REMARK REVDAT 3 30-JUN-09 2Z5V 1 JRNL REVDAT 2 24-FEB-09 2Z5V 1 VERSN REVDAT 1 05-AUG-08 2Z5V 0 JRNL AUTH H.OHNISHI,H.TOCHIO,Z.KATO,K.E.ORII,A.LI,T.KIMURA,H.HIROAKI, JRNL AUTH 2 N.KONDO,M.SHIRAKAWA JRNL TITL STRUCTURAL BASIS FOR THE MULTIPLE INTERACTIONS OF THE MYD88 JRNL TITL 2 TIR DOMAIN IN TLR4 SIGNALING. JRNL REF PROC.NATL.ACAD.SCI.USA 2009 JRNL REFN ESSN 1091-6490 JRNL PMID 19506249 JRNL DOI 10.1073/PNAS.0812956106 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE REMARK 3 -KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ,RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z5V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000027559. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 THR A 1 REMARK 465 THR A 2 REMARK 465 LEU A 3 REMARK 465 ASP A 4 REMARK 465 ASP A 5 REMARK 465 PRO A 6 REMARK 465 LEU A 7 REMARK 465 GLY A 8 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O THR A 90 H LEU A 94 1.47 REMARK 500 O PRO A 118 H ILE A 120 1.60 REMARK 500 REMARK 500 REMARK: NULL 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 MET A 10 99.56 -41.45 REMARK 500 1 PRO A 11 -167.60 -71.99 REMARK 500 1 ASP A 15 -65.42 -98.57 REMARK 500 1 ASP A 24 50.57 -150.12 REMARK 500 1 THR A 38 -179.72 -52.16 REMARK 500 1 LEU A 52 79.84 -107.48 REMARK 500 1 ARG A 68 -61.50 -97.16 REMARK 500 1 SER A 95 54.91 -107.58 REMARK 500 1 LEU A 96 -78.46 -80.32 REMARK 500 1 ALA A 100 45.76 -142.37 REMARK 500 1 GLN A 102 28.28 -150.90 REMARK 500 1 LYS A 111 163.86 176.37 REMARK 500 1 LYS A 115 -161.22 -108.70 REMARK 500 1 SER A 119 69.45 -66.73 REMARK 500 1 ILE A 120 -45.16 -148.69 REMARK 500 1 PHE A 123 31.18 -170.57 REMARK 500 1 THR A 125 98.94 -57.47 REMARK 500 1 ASN A 131 53.01 -157.11 REMARK 500 2 MET A 10 74.03 59.79 REMARK 500 2 PRO A 11 176.34 -51.37 REMARK 500 2 ASP A 15 -65.11 -92.82 REMARK 500 2 ASP A 48 -177.32 -178.33 REMARK 500 2 ARG A 49 -58.19 -125.59 REMARK 500 2 ASP A 50 74.01 -113.80 REMARK 500 2 VAL A 51 -44.31 -131.66 REMARK 500 2 SER A 95 55.76 -109.47 REMARK 500 2 LEU A 96 -78.51 -80.06 REMARK 500 2 ALA A 100 42.43 -145.37 REMARK 500 2 GLN A 102 30.86 -145.25 REMARK 500 2 LYS A 111 -170.05 170.73 REMARK 500 2 LYS A 115 -160.49 -103.46 REMARK 500 2 SER A 119 68.94 -66.74 REMARK 500 2 ILE A 120 -45.38 -149.17 REMARK 500 2 PHE A 123 27.66 -164.37 REMARK 500 2 THR A 125 101.71 -56.63 REMARK 500 3 MET A 10 83.13 55.70 REMARK 500 3 PRO A 11 -172.24 -61.42 REMARK 500 3 ASP A 15 -68.38 -93.33 REMARK 500 3 ASN A 39 35.49 -174.76 REMARK 500 3 ARG A 49 -48.33 -169.49 REMARK 500 3 ASP A 50 36.95 -174.48 REMARK 500 3 PRO A 53 173.36 -53.51 REMARK 500 3 SER A 95 53.53 -106.23 REMARK 500 3 LEU A 96 -80.51 -82.39 REMARK 500 3 LYS A 111 149.90 179.21 REMARK 500 3 LYS A 115 -160.31 -108.24 REMARK 500 3 SER A 119 70.10 -67.16 REMARK 500 3 ILE A 120 -44.55 -149.37 REMARK 500 3 PHE A 123 26.96 -165.55 REMARK 500 3 THR A 125 99.32 -58.90 REMARK 500 REMARK 500 THIS ENTRY HAS 373 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2Z5V A 1 149 UNP Q99836 MYD88_HUMAN 148 296 SEQRES 1 A 149 THR THR LEU ASP ASP PRO LEU GLY HIS MET PRO GLU ARG SEQRES 2 A 149 PHE ASP ALA PHE ILE CYS TYR CYS PRO SER ASP ILE GLN SEQRES 3 A 149 PHE VAL GLN GLU MET ILE ARG GLN LEU GLU GLN THR ASN SEQRES 4 A 149 TYR ARG LEU LYS LEU CYS VAL SER ASP ARG ASP VAL LEU SEQRES 5 A 149 PRO GLY THR CYS VAL TRP SER ILE ALA SER GLU LEU ILE SEQRES 6 A 149 GLU LYS ARG CYS ARG ARG MET VAL VAL VAL VAL SER ASP SEQRES 7 A 149 ASP TYR LEU GLN SER LYS GLU CYS ASP PHE GLN THR LYS SEQRES 8 A 149 PHE ALA LEU SER LEU SER PRO GLY ALA HIS GLN LYS ARG SEQRES 9 A 149 LEU ILE PRO ILE LYS TYR LYS ALA MET LYS LYS GLU PHE SEQRES 10 A 149 PRO SER ILE LEU ARG PHE ILE THR VAL CYS ASP TYR THR SEQRES 11 A 149 ASN PRO CYS THR LYS SER TRP PHE TRP THR ARG LEU ALA SEQRES 12 A 149 LYS ALA LEU SER LEU PRO HELIX 1 1 ASP A 24 GLN A 37 1 14 HELIX 2 2 SER A 77 GLN A 82 1 6 HELIX 3 3 SER A 83 SER A 95 1 13 HELIX 4 4 ASN A 131 SER A 136 1 6 HELIX 5 5 TRP A 137 SER A 147 1 11 SHEET 1 A 5 LEU A 44 CYS A 45 0 SHEET 2 A 5 ALA A 16 CYS A 19 1 N ILE A 18 O CYS A 45 SHEET 3 A 5 ARG A 71 VAL A 75 1 O VAL A 73 N CYS A 19 SHEET 4 A 5 LEU A 105 LYS A 109 1 O ILE A 106 N MET A 72 SHEET 5 A 5 CYS A 127 ASP A 128 1 O CYS A 127 N LYS A 109 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