HEADER DE NOVO PROTEIN 26-JUL-24 9CU8 TITLE CRYSTAL STRUCTURE OF TNFR2 TNFR2_MB1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TNFR2_MB1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 1B; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: TUMOR NECROSIS FACTOR RECEPTOR 2,TNF-R2,TUMOR NECROSIS COMPND 9 FACTOR RECEPTOR TYPE II,TNF-RII,TNFR-II,P75,P80 TNF-ALPHA RECEPTOR; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: TNFRSF1B, TNFBR, TNFR2; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DE NOVO PROTEIN, TNFR2, ANTAGONISTS AND AGONISTS, TNFR1 EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,M.GLOGL,D.BAKER REVDAT 2 18-DEC-24 9CU8 1 JRNL REVDAT 1 04-DEC-24 9CU8 0 JRNL AUTH M.GLOGL,A.KRISHNAKUMAR,R.J.RAGOTTE,I.GORESHNIK,B.COVENTRY, JRNL AUTH 2 A.K.BERA,A.KANG,E.JOYCE,G.AHN,B.HUANG,W.YANG,W.CHEN, JRNL AUTH 3 M.G.SANCHEZ,B.KOEPNICK,D.BAKER JRNL TITL TARGET-CONDITIONED DIFFUSION GENERATES POTENT TNFR JRNL TITL 2 SUPERFAMILY ANTAGONISTS AND AGONISTS. JRNL REF SCIENCE V. 386 1154 2024 JRNL REFN ESSN 1095-9203 JRNL PMID 39636970 JRNL DOI 10.1126/SCIENCE.ADP1779 REMARK 2 REMARK 2 RESOLUTION. 1.96 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 20386 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1998 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 29.1600 - 4.7200 1.00 1443 157 0.1986 0.2045 REMARK 3 2 4.7200 - 3.7500 1.00 1355 147 0.1502 0.1670 REMARK 3 3 3.7500 - 3.2800 1.00 1337 146 0.1745 0.2023 REMARK 3 4 3.2800 - 2.9800 1.00 1318 142 0.1878 0.2454 REMARK 3 5 2.9800 - 2.7600 1.00 1314 143 0.1963 0.2597 REMARK 3 6 2.7600 - 2.6000 1.00 1324 144 0.1926 0.2190 REMARK 3 7 2.6000 - 2.4700 1.00 1288 141 0.1880 0.2762 REMARK 3 8 2.4700 - 2.3600 1.00 1315 143 0.1832 0.2330 REMARK 3 9 2.3600 - 2.2700 1.00 1309 141 0.1921 0.2595 REMARK 3 10 2.2700 - 2.1900 1.00 1269 139 0.1780 0.2722 REMARK 3 11 2.1900 - 2.1300 1.00 1311 142 0.1852 0.2390 REMARK 3 12 2.1300 - 2.0600 1.00 1278 139 0.1917 0.2291 REMARK 3 13 2.0600 - 2.0100 1.00 1298 140 0.1970 0.2931 REMARK 3 14 2.0100 - 1.9600 0.96 1229 134 0.2199 0.2808 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.006 NULL REMARK 3 ANGLE : 0.799 NULL REMARK 3 CHIRALITY : 0.047 353 REMARK 3 PLANARITY : 0.008 394 REMARK 3 DIHEDRAL : 17.725 838 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 9CU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000286351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97936 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20443 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 29.160 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.72500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 44.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M IMIDAZOLE; MES MONOHYDRATE (ACID) REMARK 280 PH 6.5, 0.12 M MONOSACCHARIDES, 40% V/V PEG 500 MME; 20% W/V PEG REMARK 280 20000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 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 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 17.53550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.48650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.31050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.48650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.53550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.31050 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER B 270 REMARK 465 THR B 271 REMARK 465 SER B 272 REMARK 465 PRO B 273 REMARK 465 THR B 274 REMARK 465 ARG B 275 REMARK 465 SER B 276 REMARK 465 MET B 277 REMARK 465 ALA B 278 REMARK 465 PRO B 279 REMARK 465 GLY B 280 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O GLU B 103 OG SER B 106 2.13 REMARK 500 ND2 ASN B 261 O HOH B 301 2.17 REMARK 500 O HOH A 207 O HOH A 246 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 56 82.52 -155.02 REMARK 500 REMARK 500 REMARK: NULL DBREF 9CU8 A 1 106 PDB 9CU8 9CU8 1 106 DBREF 9CU8 B 91 280 UNP P20333 TNR1B_HUMAN 23 212 SEQRES 1 A 106 LEU ASN PRO GLU GLN VAL ALA LYS ILE GLY ALA ALA ILE SEQRES 2 A 106 ASP ALA GLY ARG LYS TYR LEU ASP ALA LYS ILE GLU GLU SEQRES 3 A 106 ALA LYS LYS THR LEU THR LEU ARG THR ALA GLN ALA LEU SEQRES 4 A 106 LEU VAL ILE ARG SER GLN TYR GLU ARG ALA VAL ASP THR SEQRES 5 A 106 LEU PHE THR ASP PRO SER ALA ALA GLU LYS GLU LEU ALA SEQRES 6 A 106 ALA THR LEU ALA THR ILE ASP ARG LEU LEU LYS GLU HIS SEQRES 7 A 106 PRO GLU LEU ALA ALA GLU ILE LYS ALA PHE ILE ARG SER SEQRES 8 A 106 THR MET ALA GLU ILE ARG ALA LEU LEU ALA ALA SER LEU SEQRES 9 A 106 ALA ALA SEQRES 1 B 190 LEU PRO ALA GLN VAL ALA PHE THR PRO TYR ALA PRO GLU SEQRES 2 B 190 PRO GLY SER THR CYS ARG LEU ARG GLU TYR TYR ASP GLN SEQRES 3 B 190 THR ALA GLN MET CYS CYS SER LYS CYS SER PRO GLY GLN SEQRES 4 B 190 HIS ALA LYS VAL PHE CYS THR LYS THR SER ASP THR VAL SEQRES 5 B 190 CYS ASP SER CYS GLU ASP SER THR TYR THR GLN LEU TRP SEQRES 6 B 190 ASN TRP VAL PRO GLU CYS LEU SER CYS GLY SER ARG CYS SEQRES 7 B 190 SER SER ASP GLN VAL GLU THR GLN ALA CYS THR ARG GLU SEQRES 8 B 190 GLN ASN ARG ILE CYS THR CYS ARG PRO GLY TRP TYR CYS SEQRES 9 B 190 ALA LEU SER LYS GLN GLU GLY CYS ARG LEU CYS ALA PRO SEQRES 10 B 190 LEU ARG LYS CYS ARG PRO GLY PHE GLY VAL ALA ARG PRO SEQRES 11 B 190 GLY THR GLU THR SER ASP VAL VAL CYS LYS PRO CYS ALA SEQRES 12 B 190 PRO GLY THR PHE SER ASN THR THR SER SER THR ASP ILE SEQRES 13 B 190 CYS ARG PRO HIS GLN ILE CYS ASN VAL VAL ALA ILE PRO SEQRES 14 B 190 GLY ASN ALA SER MET ASP ALA VAL CYS THR SER THR SER SEQRES 15 B 190 PRO THR ARG SER MET ALA PRO GLY FORMUL 3 HOH *186(H2 O) HELIX 1 AA1 ASN A 2 THR A 30 1 29 HELIX 2 AA2 THR A 32 ASP A 56 1 25 HELIX 3 AA3 ALA A 59 LEU A 75 1 17 HELIX 4 AA4 HIS A 78 ALA A 105 1 28 SHEET 1 AA1 2 GLU B 112 ASP B 115 0 SHEET 2 AA1 2 MET B 120 SER B 123 -1 O MET B 120 N ASP B 115 SHEET 1 AA2 2 GLN B 129 VAL B 133 0 SHEET 2 AA2 2 VAL B 142 SER B 145 -1 O VAL B 142 N VAL B 133 SHEET 1 AA3 2 THR B 150 TYR B 151 0 SHEET 2 AA3 2 LEU B 162 SER B 163 -1 O LEU B 162 N TYR B 151 SHEET 1 AA4 2 VAL B 173 GLN B 176 0 SHEET 2 AA4 2 ILE B 185 THR B 187 -1 O THR B 187 N VAL B 173 SHEET 1 AA5 2 TRP B 192 SER B 197 0 SHEET 2 AA5 2 CYS B 202 PRO B 207 -1 O ALA B 206 N TYR B 193 SHEET 1 AA6 2 PHE B 215 ARG B 219 0 SHEET 2 AA6 2 VAL B 228 PRO B 231 -1 O VAL B 228 N ALA B 218 SHEET 1 AA7 2 THR B 236 PHE B 237 0 SHEET 2 AA7 2 ARG B 248 PRO B 249 -1 O ARG B 248 N PHE B 237 SHEET 1 AA8 2 VAL B 256 ILE B 258 0 SHEET 2 AA8 2 VAL B 267 CYS B 268 -1 O VAL B 267 N ILE B 258 SSBOND 1 CYS B 108 CYS B 121 1555 1555 2.05 SSBOND 2 CYS B 122 CYS B 135 1555 1555 2.03 SSBOND 3 CYS B 125 CYS B 143 1555 1555 2.04 SSBOND 4 CYS B 146 CYS B 161 1555 1555 2.03 SSBOND 5 CYS B 164 CYS B 178 1555 1555 2.05 SSBOND 6 CYS B 168 CYS B 186 1555 1555 2.03 SSBOND 7 CYS B 188 CYS B 205 1555 1555 2.03 SSBOND 8 CYS B 194 CYS B 202 1555 1555 2.06 SSBOND 9 CYS B 211 CYS B 229 1555 1555 2.04 SSBOND 10 CYS B 232 CYS B 247 1555 1555 2.06 SSBOND 11 CYS B 253 CYS B 268 1555 1555 2.03 CISPEP 1 THR B 98 PRO B 99 0 -0.06 CRYST1 35.071 74.621 104.973 90.00 90.00 90.00 P 21 21 21 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 0.028514 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013401 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009526 0.00000