HEADER IMMUNE SYSTEM 09-SEP-24 9DKI TITLE CRYSTAL STRUCTURE OF THE TIR DOMAIN C117H MUTANT FROM HUMAN TRAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: TIR DOMAIN-CONTAINING ADAPTER MOLECULE 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TIR DOMAIN; COMPND 5 SYNONYM: TICAM-2,PUTATIVE NF-KAPPA-B-ACTIVATING PROTEIN 502,TRIF- COMPND 6 RELATED ADAPTER MOLECULE,TRAM,TOLL-LIKE RECEPTOR ADAPTOR PROTEIN 3, COMPND 7 TOLL/INTERLEUKIN-1 RECEPTOR DOMAIN-CONTAINING PROTEIN,MYD88-4; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TICAM2, TIRAP3, TIRP, TRAM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TOLL-LIKE RECEPTOR, TIR DOMAIN, TRAM, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.PAN,W.GU,J.D.NANSON,B.KOBE REVDAT 1 22-JAN-25 9DKI 0 JRNL AUTH M.K.MANIK,M.PAN,L.XIAO,W.GU,H.KIM,S.POSPICH,A.HEDGER, JRNL AUTH 2 P.R.VAJJHALA,M.Y.L.LEE,X.QIAN,M.J.LANDSBERG,T.VE,J.D.NANSON, JRNL AUTH 3 S.RAUNSER,K.J.STACEY,H.WU,B.KOBE JRNL TITL STRUCTURAL BASIS FOR TIR DOMAIN-MEDIATED INNATE IMMUNE JRNL TITL 2 SIGNALING BY TOLL-LIKE RECEPTOR ADAPTORS TRIF AND TRAM. JRNL REF PROC.NATL.ACAD.SCI.USA V. 122 88122 2025 JRNL REFN ESSN 1091-6490 JRNL PMID 39786929 JRNL DOI 10.1073/PNAS.2418988122 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 4567 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.410 REMARK 3 FREE R VALUE TEST SET COUNT : 247 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 35.5300 - 3.7800 1.00 2230 107 0.2257 0.2407 REMARK 3 2 3.7800 - 3.0000 0.99 2090 140 0.2608 0.3509 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.108 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.555 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 116.0 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 : 0.003 1181 REMARK 3 ANGLE : 0.652 1604 REMARK 3 CHIRALITY : 0.045 175 REMARK 3 PLANARITY : 0.007 213 REMARK 3 DIHEDRAL : 12.771 440 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 9DKI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1000288244. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.954 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4567 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 35.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 38.70 REMARK 200 R MERGE (I) : 0.06086 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 42.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.72500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.440 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LI2SO4, 0.1 M BIS-TRIS (PH 6.5) REMARK 280 AND 16% W/V PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 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 43.51050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.51050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.51050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.51050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.51050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.51050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 43.51050 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 43.51050 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 43.51050 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 43.51050 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 43.51050 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 43.51050 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 43.51050 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 43.51050 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 43.51050 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 43.51050 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 43.51050 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 43.51050 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 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 DBREF 9DKI A 78 217 UNP Q86XR7 TCAM2_HUMAN 78 217 SEQADV 9DKI HIS A 117 UNP Q86XR7 CYS 117 ENGINEERED MUTATION SEQRES 1 A 140 PHE LEU LYS PHE VAL ILE LEU HIS ALA GLU ASP ASP THR SEQRES 2 A 140 ASP GLU ALA LEU ARG VAL GLN ASN LEU LEU GLN ASP ASP SEQRES 3 A 140 PHE GLY ILE LYS PRO GLY ILE ILE PHE ALA GLU MET PRO SEQRES 4 A 140 HIS GLY ARG GLN HIS LEU GLN ASN LEU ASP ASP ALA VAL SEQRES 5 A 140 ASN GLY SER ALA TRP THR ILE LEU LEU LEU THR GLU ASN SEQRES 6 A 140 PHE LEU ARG ASP THR TRP CYS ASN PHE GLN PHE TYR THR SEQRES 7 A 140 SER LEU MET ASN SER VAL ASN ARG GLN HIS LYS TYR ASN SEQRES 8 A 140 SER VAL ILE PRO MET ARG PRO LEU ASN ASN PRO LEU PRO SEQRES 9 A 140 ARG GLU ARG THR PRO PHE ALA LEU GLN THR ILE ASN ALA SEQRES 10 A 140 LEU GLU GLU GLU SER ARG GLY PHE PRO THR GLN VAL GLU SEQRES 11 A 140 ARG ILE PHE GLN GLU SER VAL TYR LYS THR HELIX 1 AA1 ALA A 86 ASP A 88 5 3 HELIX 2 AA2 ASP A 89 ASP A 103 1 15 HELIX 3 AA3 ALA A 113 MET A 115 5 3 HELIX 4 AA4 GLN A 120 GLY A 131 1 12 HELIX 5 AA5 THR A 140 THR A 147 1 8 HELIX 6 AA6 THR A 147 SER A 160 1 14 HELIX 7 AA7 HIS A 165 ASN A 168 5 4 HELIX 8 AA8 PRO A 181 THR A 185 5 5 HELIX 9 AA9 PRO A 186 THR A 191 1 6 HELIX 10 AB1 GLY A 201 PHE A 210 1 10 HELIX 11 AB2 GLN A 211 TYR A 215 5 5 SHEET 1 AA1 5 GLY A 109 ILE A 111 0 SHEET 2 AA1 5 LEU A 79 LEU A 84 1 N ILE A 83 O ILE A 110 SHEET 3 AA1 5 SER A 132 LEU A 138 1 O ILE A 136 N VAL A 82 SHEET 4 AA1 5 VAL A 170 ARG A 174 1 O MET A 173 N LEU A 137 SHEET 5 AA1 5 LEU A 195 GLU A 196 1 O LEU A 195 N PRO A 172 CISPEP 1 LYS A 107 PRO A 108 0 2.87 CRYST1 87.021 87.021 87.021 90.00 90.00 90.00 P 21 3 12 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 0.011491 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011491 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011491 0.00000 TER 1154 THR A 217 MASTER 221 0 0 11 5 0 0 6 1153 1 0 11 END