HEADER SIGNALING PROTEIN 15-MAR-21 7NUW TITLE CRYSTAL STRUCTURE OF THE TIR DOMAIN OF HUMAN TLR1 (CRYSTALLISED WITH TITLE 2 ZN2+ IONS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOLL-LIKE RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TOLL/INTERLEUKIN-1 RECEPTOR-LIKE PROTEIN,TIL; COMPND 5 EC: 3.2.2.6; COMPND 6 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: TLR1, KIAA0012; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PGEMEX-1 KEYWDS TOLL-LIKE RECEPTOR, TIR DOMAIN, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.D.VAKHRAMEEV,A.P.LUGININA,M.B.SHEVTSOV,V.A.LUSHPA,K.S.MINEEV, AUTHOR 2 V.I.BORSHCHEVSKIY REVDAT 4 16-OCT-24 7NUW 1 REMARK REVDAT 3 31-JAN-24 7NUW 1 REMARK REVDAT 2 13-OCT-21 7NUW 1 JRNL REVDAT 1 25-AUG-21 7NUW 0 JRNL AUTH V.A.LUSHPA,M.V.GONCHARUK,C.LIN,A.O.ZALEVSKY,I.A.TALYZINA, JRNL AUTH 2 A.P.LUGININA,D.D.VAKHRAMEEV,M.B.SHEVTSOV,S.A.GONCHARUK, JRNL AUTH 3 A.S.ARSENIEV,V.I.BORSHCHEVSKIY,X.WANG,K.S.MINEEV JRNL TITL MODULATION OF TOLL-LIKE RECEPTOR 1 INTRACELLULAR DOMAIN JRNL TITL 2 STRUCTURE AND ACTIVITY BY ZN 2+ IONS. JRNL REF COMMUN BIOL V. 4 1003 2021 JRNL REFN ESSN 2399-3642 JRNL PMID 34429510 JRNL DOI 10.1038/S42003-021-02532-0 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16969 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 851 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 2.0200 - 1.9000 0.99 2612 139 0.3578 0.3971 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) : 0.288 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.480 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.34 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 1332 REMARK 3 ANGLE : 0.498 1812 REMARK 3 CHIRALITY : 0.044 197 REMARK 3 PLANARITY : 0.004 227 REMARK 3 DIHEDRAL : 16.158 479 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 7NUW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114554. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.972 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17010 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 43.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 38.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.690 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: 1FYV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 170 MM AMMONIUM ACETATE, 85 MM SODIUM REMARK 280 CITRATE TRIBASIC DIHYDRATE PH 5.6, 25.5% W/V POLYETHYLENE GLYCOL REMARK 280 4,000, 15% V/V GLYCEROL (#9 FROM HR2-122 HAMPTON) + ZINC REMARK 280 CHLORIDE(MOLAR RATIO ZINC CHLORIDE:PROTEIN 1:1). GROWTH AT +4 REMARK 280 FOR 3-4 MONTHS., VAPOR DIFFUSION, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.90667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.95333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 45.90667 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.95333 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.90667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 22.95333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 45.90667 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 22.95333 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: 8650 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 GLN A 783 REMARK 465 ALA A 784 REMARK 465 LYS A 785 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 634 CG OD1 ND2 REMARK 470 LYS A 661 CG CD CE NZ REMARK 470 GLU A 670 CG CD OE1 OE2 REMARK 470 ASN A 717 CG OD1 ND2 REMARK 470 LEU A 718 CD1 CD2 REMARK 470 GLU A 721 CG CD OE1 OE2 REMARK 470 ARG A 752 NE CZ NH1 NH2 REMARK 470 ARG A 753 CD NE CZ NH1 NH2 REMARK 470 LYS A 760 CG CD CE NZ REMARK 470 LYS A 762 CD CE NZ REMARK 470 GLU A 782 CD OE1 OE2 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 GLU A 670 -12.03 78.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 7NUW A 625 785 UNP Q15399 TLR1_HUMAN 625 785 SEQADV 7NUW SER A 624 UNP Q15399 EXPRESSION TAG SEQRES 1 A 162 SER ASN ILE PRO LEU GLU GLU LEU GLN ARG ASN LEU GLN SEQRES 2 A 162 PHE HIS ALA PHE ILE SER TYR SER GLY HIS ASP SER PHE SEQRES 3 A 162 TRP VAL LYS ASN GLU LEU LEU PRO ASN LEU GLU LYS GLU SEQRES 4 A 162 GLY MET GLN ILE CYS LEU HIS GLU ARG ASN PHE VAL PRO SEQRES 5 A 162 GLY LYS SER ILE VAL GLU ASN ILE ILE THR CYS ILE GLU SEQRES 6 A 162 LYS SER TYR LYS SER ILE PHE VAL LEU SER PRO ASN PHE SEQRES 7 A 162 VAL GLN SER GLU TRP CYS HIS TYR GLU LEU TYR PHE ALA SEQRES 8 A 162 HIS HIS ASN LEU PHE HIS GLU GLY SER ASN SER LEU ILE SEQRES 9 A 162 LEU ILE LEU LEU GLU PRO ILE PRO GLN TYR SER ILE PRO SEQRES 10 A 162 SER SER TYR HIS LYS LEU LYS SER LEU MET ALA ARG ARG SEQRES 11 A 162 THR TYR LEU GLU TRP PRO LYS GLU LYS SER LYS ARG GLY SEQRES 12 A 162 LEU PHE TRP ALA ASN LEU ARG ALA ALA ILE ASN ILE LYS SEQRES 13 A 162 LEU THR GLU GLN ALA LYS FORMUL 2 HOH *39(H2 O) HELIX 1 AA1 PRO A 627 LEU A 631 5 5 HELIX 2 AA2 SER A 644 HIS A 646 5 3 HELIX 3 AA3 ASP A 647 GLU A 654 1 8 HELIX 4 AA4 GLU A 654 LYS A 661 1 8 HELIX 5 AA5 SER A 678 LYS A 689 1 12 HELIX 6 AA6 SER A 698 GLU A 705 1 8 HELIX 7 AA7 GLU A 705 ALA A 714 1 10 HELIX 8 AA8 PRO A 735 ILE A 739 5 5 HELIX 9 AA9 TYR A 743 ARG A 752 1 10 HELIX 10 AB1 GLU A 761 SER A 763 5 3 HELIX 11 AB2 LYS A 764 ILE A 778 1 15 SHEET 1 AA1 5 ILE A 666 LEU A 668 0 SHEET 2 AA1 5 PHE A 637 SER A 642 1 N ALA A 639 O CYS A 667 SHEET 3 AA1 5 SER A 690 LEU A 697 1 O ILE A 694 N PHE A 640 SHEET 4 AA1 5 LEU A 726 LEU A 730 1 O ILE A 727 N SER A 693 SHEET 5 AA1 5 LEU A 756 GLU A 757 1 O LEU A 756 N LEU A 728 SSBOND 1 CYS A 667 CYS A 686 1555 1555 2.04 SSBOND 2 CYS A 707 CYS A 707 1555 8675 2.04 CRYST1 101.516 101.516 68.860 90.00 90.00 120.00 P 62 2 2 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 0.009851 0.005687 0.000000 0.00000 SCALE2 0.000000 0.011375 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014522 0.00000