HEADER PROTEIN BINDING 24-DEC-20 7BER TITLE SFX STRUCTURE OF THE MYD88 TIR DOMAIN HIGHER-ORDER ASSEMBLY (SOLVED, TITLE 2 REBUILT AND REFINED USING AN IDENTICAL PROTOCOL TO THE MICROED TITLE 3 STRUCTURE OF THE MYD88 TIR DOMAIN HIGHER-ORDER ASSEMBLY) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYELOID DIFFERENTIATION PRIMARY RESPONSE PROTEIN MYD88; COMPND 3 CHAIN: A; COMPND 4 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 BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS SFX, SERIAL FEMTOSECOND CRYSTALLOGRAPHY, MYD88, TIR DOMAIN, HIGHER- KEYWDS 2 ORDER ASSEMBLY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.T.B.CLABBERS,S.HOLMES,T.W.MUUSSE,P.VAJJHALA,S.J.THYGESEN,A.K.MALDE, AUTHOR 2 D.J.B.HUNTER,T.I.CROLL,J.D.NANSON,M.H.RAHAMAN,A.AQUILA,M.S.HUNTER, AUTHOR 3 M.LIANG,C.H.YOON,J.ZHAO,N.A.ZATSEPIN,B.ABBEY,E.SIERECKI,Y.GAMBIN, AUTHOR 4 C.DARMANIN,B.KOBE,H.XU,T.VE REVDAT 4 31-JAN-24 7BER 1 REMARK REVDAT 3 13-DEC-23 7BER 1 REMARK REVDAT 2 26-MAY-21 7BER 1 JRNL REVDAT 1 10-MAR-21 7BER 0 JRNL AUTH M.T.B.CLABBERS,S.HOLMES,T.W.MUUSSE,P.R.VAJJHALA, JRNL AUTH 2 S.J.THYGESEN,A.K.MALDE,D.J.B.HUNTER,T.I.CROLL,L.FLUECKIGER, JRNL AUTH 3 J.D.NANSON,M.H.RAHAMAN,A.AQUILA,M.S.HUNTER,M.LIANG,C.H.YOON, JRNL AUTH 4 J.ZHAO,N.A.ZATSEPIN,B.ABBEY,E.SIERECKI,Y.GAMBIN,K.J.STACEY, JRNL AUTH 5 C.DARMANIN,B.KOBE,H.XU,T.VE JRNL TITL MYD88 TIR DOMAIN HIGHER-ORDER ASSEMBLY INTERACTIONS REVEALED JRNL TITL 2 BY MICROCRYSTAL ELECTRON DIFFRACTION AND SERIAL FEMTOSECOND JRNL TITL 3 CRYSTALLOGRAPHY. JRNL REF NAT COMMUN V. 12 2578 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33972532 JRNL DOI 10.1038/S41467-021-22590-6 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 7040 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.239 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 353 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 30.9300 - 3.3200 1.00 2422 128 0.1972 0.2276 REMARK 3 2 3.3200 - 2.6300 0.99 2299 121 0.2948 0.3372 REMARK 3 3 2.6300 - 2.3000 0.84 1966 104 0.3178 0.4073 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.267 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.873 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.001 1159 REMARK 3 ANGLE : 0.370 1565 REMARK 3 CHIRALITY : 0.039 174 REMARK 3 PLANARITY : 0.003 195 REMARK 3 DIHEDRAL : 9.888 713 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7BER COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292113093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-15 REMARK 200 TEMPERATURE (KELVIN) : 300 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : CXI REMARK 200 X-RAY GENERATOR MODEL : SLAC LCLS BEAMLINE CXI REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : CS-PAD CXI-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7118 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 1.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.1 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.2 REMARK 200 STARTING MODEL: 4W8G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MAL TIR (0.5-3 MM) INCUBATED WITH REMARK 280 MYD88 TIR (60-100 MM) IN 10 MM HEPES PH 7.5-8, 150 MM NACL AT REMARK 280 310K, BATCH MODE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.20000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.20000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 154 REMARK 465 GLY A 155 REMARK 465 HIS A 156 REMARK 465 MET A 157 REMARK 465 PRO A 158 REMARK 465 LEU A 297 REMARK 465 GLU A 298 REMARK 465 HIS A 299 REMARK 465 HIS A 300 REMARK 465 HIS A 301 REMARK 465 HIS A 302 REMARK 465 HIS A 303 REMARK 465 HIS A 304 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 THR A 185 -166.69 -111.49 REMARK 500 SER A 244 79.74 -161.21 REMARK 500 REMARK 500 REMARK: NULL DBREF 7BER A 155 296 UNP Q99836 MYD88_HUMAN 155 296 SEQADV 7BER MET A 154 UNP Q99836 INITIATING METHIONINE SEQADV 7BER LEU A 297 UNP Q99836 EXPRESSION TAG SEQADV 7BER GLU A 298 UNP Q99836 EXPRESSION TAG SEQADV 7BER HIS A 299 UNP Q99836 EXPRESSION TAG SEQADV 7BER HIS A 300 UNP Q99836 EXPRESSION TAG SEQADV 7BER HIS A 301 UNP Q99836 EXPRESSION TAG SEQADV 7BER HIS A 302 UNP Q99836 EXPRESSION TAG SEQADV 7BER HIS A 303 UNP Q99836 EXPRESSION TAG SEQADV 7BER HIS A 304 UNP Q99836 EXPRESSION TAG SEQRES 1 A 151 MET GLY HIS MET PRO GLU ARG PHE ASP ALA PHE ILE CYS SEQRES 2 A 151 TYR CYS PRO SER ASP ILE GLN PHE VAL GLN GLU MET ILE SEQRES 3 A 151 ARG GLN LEU GLU GLN THR ASN TYR ARG LEU LYS LEU CYS SEQRES 4 A 151 VAL SER ASP ARG ASP VAL LEU PRO GLY THR CYS VAL TRP SEQRES 5 A 151 SER ILE ALA SER GLU LEU ILE GLU LYS ARG CYS ARG ARG SEQRES 6 A 151 MET VAL VAL VAL VAL SER ASP ASP TYR LEU GLN SER LYS SEQRES 7 A 151 GLU CYS ASP PHE GLN THR LYS PHE ALA LEU SER LEU SER SEQRES 8 A 151 PRO GLY ALA HIS GLN LYS ARG LEU ILE PRO ILE LYS TYR SEQRES 9 A 151 LYS ALA MET LYS LYS GLU PHE PRO SER ILE LEU ARG PHE SEQRES 10 A 151 ILE THR VAL CYS ASP TYR THR ASN PRO CYS THR LYS SER SEQRES 11 A 151 TRP PHE TRP THR ARG LEU ALA LYS ALA LEU SER LEU PRO SEQRES 12 A 151 LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 CYS A 168 SER A 170 5 3 HELIX 2 AA2 ASP A 171 GLU A 183 1 13 HELIX 3 AA3 VAL A 193 VAL A 198 1 6 HELIX 4 AA4 CYS A 203 ARG A 215 1 13 HELIX 5 AA5 SER A 224 GLN A 229 1 6 HELIX 6 AA6 SER A 230 SER A 244 1 15 HELIX 7 AA7 PRO A 265 ARG A 269 5 5 HELIX 8 AA8 THR A 281 SER A 283 5 3 HELIX 9 AA9 TRP A 284 LEU A 293 1 10 SHEET 1 AA1 5 LEU A 191 CYS A 192 0 SHEET 2 AA1 5 PHE A 161 CYS A 166 1 N ALA A 163 O CYS A 192 SHEET 3 AA1 5 CYS A 216 VAL A 223 1 O VAL A 220 N CYS A 166 SHEET 4 AA1 5 LEU A 252 LYS A 256 1 O ILE A 255 N VAL A 221 SHEET 5 AA1 5 CYS A 274 ASP A 275 1 O CYS A 274 N PRO A 254 CRYST1 100.400 31.500 54.500 90.00 107.40 90.00 C 1 2 1 4 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 0.009960 0.000000 0.003121 0.00000 SCALE2 0.000000 0.031746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019229 0.00000