HEADER SIGNALING PROTEIN 17-JUL-20 6ZSZ TITLE CRYSTAL STRUCTURE OF THE GRINDELWALD EXTRACELLULAR DOMAIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN GRINDELWALD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: GRND, CG10176; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TNF RECEPTOR, JNK CASCADE, TNF, SIGNALING, EXTRACELLULAR, TUMOR KEYWDS 2 NECROSIS FACTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR V.PALMERINI,V.CECATIELLO,S.PASQUALATO,M.MAPELLI REVDAT 2 13-OCT-21 6ZSZ 1 JRNL REVDAT 1 31-MAR-21 6ZSZ 0 JRNL AUTH V.PALMERINI,S.MONZANI,Q.LAURICHESSE,R.LOUDHAIEF,S.MARI, JRNL AUTH 2 V.CECATIELLO,V.OLIERIC,S.PASQUALATO,J.COLOMBANI, JRNL AUTH 3 D.S.ANDERSEN,M.MAPELLI JRNL TITL DROSOPHILA TNFRS GRINDELWALD AND WENGEN BIND EIGER WITH JRNL TITL 2 DIFFERENT AFFINITIES AND PROMOTE DISTINCT CELLULAR JRNL TITL 3 FUNCTIONS. JRNL REF NAT COMMUN V. 12 2070 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 33824334 JRNL DOI 10.1038/S41467-021-22080-9 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19_4092 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.94 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.540 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 3976 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 675 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 29.9400 - 3.2900 1.00 1305 146 0.1703 0.2303 REMARK 3 2 3.2800 - 2.6100 1.00 1265 137 0.1733 0.1724 REMARK 3 3 2.6100 - 2.2800 1.00 1301 138 0.1658 0.2074 REMARK 3 4 2.2800 - 2.0700 0.99 1261 145 0.1532 0.2062 REMARK 3 5 2.0700 - 1.9200 0.73 939 109 0.1507 0.2048 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.58 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 : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 34 THROUGH 52 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.5018 15.4035 43.5543 REMARK 3 T TENSOR REMARK 3 T11: 0.0637 T22: 0.0510 REMARK 3 T33: 0.0529 T12: 0.0214 REMARK 3 T13: -0.0145 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 1.0573 L22: 0.3549 REMARK 3 L33: 0.9997 L12: 0.2362 REMARK 3 L13: 0.1600 L23: 0.0985 REMARK 3 S TENSOR REMARK 3 S11: 0.0446 S12: 0.0765 S13: -0.1269 REMARK 3 S21: -0.0766 S22: -0.0781 S23: 0.1023 REMARK 3 S31: -0.1021 S32: -0.0261 S33: 0.0073 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 53 THROUGH 61 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.7410 17.8572 35.7080 REMARK 3 T TENSOR REMARK 3 T11: 0.1431 T22: 0.0952 REMARK 3 T33: 0.0630 T12: -0.0544 REMARK 3 T13: 0.0225 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 2.8345 L22: 0.9646 REMARK 3 L33: 2.6306 L12: -0.5497 REMARK 3 L13: 2.2611 L23: 0.4044 REMARK 3 S TENSOR REMARK 3 S11: -0.3358 S12: 0.2686 S13: 0.2538 REMARK 3 S21: -0.3100 S22: 0.0293 S23: -0.0916 REMARK 3 S31: -0.5158 S32: 0.2645 S33: 0.0740 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 62 THROUGH 76 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.5490 12.0701 29.3719 REMARK 3 T TENSOR REMARK 3 T11: 0.0906 T22: 0.0960 REMARK 3 T33: 0.0594 T12: -0.0735 REMARK 3 T13: -0.0464 T23: 0.0134 REMARK 3 L TENSOR REMARK 3 L11: 2.3149 L22: 2.4493 REMARK 3 L33: 2.5048 L12: 0.8980 REMARK 3 L13: -1.2515 L23: -1.0929 REMARK 3 S TENSOR REMARK 3 S11: 0.0066 S12: -0.1707 S13: -0.0357 REMARK 3 S21: 0.1883 S22: -0.1753 S23: -0.2633 REMARK 3 S31: -0.2429 S32: 0.3949 S33: 0.0210 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 77 THROUGH 81 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.0466 11.2977 34.3823 REMARK 3 T TENSOR REMARK 3 T11: 0.1160 T22: 0.1749 REMARK 3 T33: 0.1849 T12: -0.0296 REMARK 3 T13: 0.0034 T23: 0.0025 REMARK 3 L TENSOR REMARK 3 L11: 7.1330 L22: 2.2891 REMARK 3 L33: 5.0922 L12: 1.5830 REMARK 3 L13: -3.7170 L23: 1.6476 REMARK 3 S TENSOR REMARK 3 S11: 0.1270 S12: -0.0461 S13: 0.0772 REMARK 3 S21: 0.0189 S22: -0.0833 S23: 0.2332 REMARK 3 S31: -0.2799 S32: -0.4290 S33: -0.0864 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 6ZSZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292110144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 2.0751 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4051 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 48.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 221.8 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 163.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 5.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.04000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 45 % MPD, 0.2 M REMARK 280 AMMONIUM ACETATE CONCENTRATION 82 MG/ML, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 48.87500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 15.72500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 15.72500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.43750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 15.72500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 15.72500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 73.31250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 15.72500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.72500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.43750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 15.72500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.72500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 73.31250 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 48.87500 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 GLY A 30 REMARK 465 GLU A 31 REMARK 465 SER A 32 REMARK 465 ARG A 33 DBREF 6ZSZ A 30 81 UNP Q9VJ83 GRND_DROME 30 81 SEQRES 1 A 52 GLY GLU SER ARG ASP CYS HIS GLY THR ILE CYS HIS PRO SEQRES 2 A 52 VAL ASN GLU PHE CYS TYR VAL ALA THR GLU ARG CYS HIS SEQRES 3 A 52 PRO CYS ILE GLU VAL CYS ASN ASN GLN THR HIS ASN TYR SEQRES 4 A 52 ASP ALA PHE LEU CYS ALA LYS GLU CYS SER ALA TYR LYS FORMUL 2 HOH *48(H2 O) HELIX 1 AA1 ASP A 34 THR A 38 5 5 HELIX 2 AA2 CYS A 57 ASN A 62 1 6 HELIX 3 AA3 ASP A 69 CYS A 77 1 9 SHEET 1 AA1 2 GLU A 45 TYR A 48 0 SHEET 2 AA1 2 ARG A 53 PRO A 56 -1 O HIS A 55 N PHE A 46 SSBOND 1 CYS A 35 CYS A 47 1555 1555 2.06 SSBOND 2 CYS A 40 CYS A 54 1555 1555 2.01 SSBOND 3 CYS A 57 CYS A 77 1555 1555 2.15 SSBOND 4 CYS A 61 CYS A 73 1555 1555 2.11 CRYST1 31.450 31.450 97.750 90.00 90.00 90.00 P 41 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 0.031797 0.000000 0.000000 0.00000 SCALE2 0.000000 0.031797 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010230 0.00000