HEADER IMMUNE SYSTEM 15-JUL-21 7FD3 TITLE IL-1RAPL2 TIR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: X-LINKED INTERLEUKIN-1 RECEPTOR ACCESSORY PROTEIN-LIKE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IL-1 RECEPTOR ACCESSORY PROTEIN-LIKE 2,IL-1-RAPL-2,IL-1RAPL- COMPND 5 2,IL1RAPL-2; COMPND 6 EC: 3.2.2.6; COMPND 7 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: IL1RAPL2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS IL-1 FAMILY RECEPTOR PROTEIN, TIR DOMAIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR X.WANG,J.ZHOU REVDAT 3 29-NOV-23 7FD3 1 REMARK REVDAT 2 10-AUG-22 7FD3 1 JRNL REVDAT 1 20-JUL-22 7FD3 0 JRNL AUTH J.ZHOU,Y.XIAO,Y.REN,J.GE,X.WANG JRNL TITL STRUCTURAL BASIS OF THE IL-1 RECEPTOR TIR DOMAIN-MEDIATED JRNL TITL 2 IL-1 SIGNALING JRNL REF ISCIENCE V. 25 04508 2022 JRNL REFN ESSN 2589-0042 JRNL DOI 10.1016/J.ISCI.2022.104508 REMARK 2 REMARK 2 RESOLUTION. 2.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 5437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 268 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 49.2900 - 3.7700 0.99 2694 117 0.2314 0.2583 REMARK 3 2 3.7700 - 2.9900 0.99 2475 151 0.2723 0.3517 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.840 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.42 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7FD3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023295. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-18 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5452 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.990 REMARK 200 RESOLUTION RANGE LOW (A) : 49.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 24.00 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.71600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1T3G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 8% V/V TACSIMATE PH5.0, 12% W/V REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.38950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 25.57050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 25.57050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 138.58425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 25.57050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 25.57050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.19475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 25.57050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 25.57050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 138.58425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 25.57050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 25.57050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.19475 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 92.38950 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 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 GLN A 413 REMARK 465 ASP A 414 REMARK 465 THR A 415 REMARK 465 LEU A 416 REMARK 465 ASP A 417 REMARK 465 LYS A 560 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 PRO A 421 -123.47 -92.24 REMARK 500 GLU A 429 -72.69 -102.39 REMARK 500 ARG A 482 69.78 23.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 448 ASP A 449 -146.77 REMARK 500 REMARK 500 REMARK: NULL DBREF 7FD3 A 400 560 UNP Q9NP60 IRPL2_HUMAN 400 560 SEQRES 1 A 161 LYS GLU TYR ASP ALA TYR LEU SER TYR THR LYS VAL ASP SEQRES 2 A 161 GLN ASP THR LEU ASP CYS ASP ASN PRO GLU GLU GLU GLN SEQRES 3 A 161 PHE ALA LEU GLU VAL LEU PRO ASP VAL LEU GLU LYS HIS SEQRES 4 A 161 TYR GLY TYR LYS LEU PHE ILE PRO GLU ARG ASP LEU ILE SEQRES 5 A 161 PRO SER GLY THR TYR MET GLU ASP LEU THR ARG TYR VAL SEQRES 6 A 161 GLU GLN SER ARG ARG LEU ILE ILE VAL LEU THR PRO ASP SEQRES 7 A 161 TYR ILE LEU ARG ARG GLY TRP SER ILE PHE GLU LEU GLU SEQRES 8 A 161 SER ARG LEU HIS ASN MET LEU VAL SER GLY GLU ILE LYS SEQRES 9 A 161 VAL ILE LEU ILE GLU CYS THR GLU LEU LYS GLY LYS VAL SEQRES 10 A 161 ASN CYS GLN GLU VAL GLU SER LEU LYS ARG SER ILE LYS SEQRES 11 A 161 LEU LEU SER LEU ILE LYS TRP LYS GLY SER LYS SER SER SEQRES 12 A 161 LYS LEU ASN SER LYS PHE TRP LYS HIS LEU VAL TYR GLU SEQRES 13 A 161 MET PRO ILE LYS LYS HELIX 1 AA1 PRO A 421 GLU A 429 1 9 HELIX 2 AA2 GLU A 429 LYS A 437 1 9 HELIX 3 AA3 ILE A 445 LEU A 450 1 6 HELIX 4 AA4 THR A 455 GLN A 466 1 12 HELIX 5 AA5 THR A 475 ARG A 481 1 7 HELIX 6 AA6 SER A 485 GLU A 490 1 6 HELIX 7 AA7 GLU A 490 SER A 499 1 10 HELIX 8 AA8 GLY A 514 ILE A 528 1 15 HELIX 9 AA9 GLY A 538 LYS A 543 1 6 HELIX 10 AB1 SER A 546 TYR A 554 1 9 SHEET 1 AA1 5 LEU A 443 PHE A 444 0 SHEET 2 AA1 5 ALA A 404 SER A 407 1 N ALA A 404 O PHE A 444 SHEET 3 AA1 5 ARG A 469 LEU A 474 1 O ILE A 471 N TYR A 405 SHEET 4 AA1 5 LYS A 503 GLU A 508 1 O ILE A 505 N LEU A 470 SHEET 5 AA1 5 LEU A 531 LYS A 535 1 O ILE A 534 N GLU A 508 CRYST1 51.141 51.141 184.779 90.00 90.00 90.00 P 43 21 2 8 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 0.019554 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019554 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005412 0.00000