HEADER APOPTOSIS 17-JUL-22 8DPX TITLE PRELIGAND ASSOCIATION STRUCTURE OF DR5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 10B; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: DEATH RECEPTOR 5,TNF-RELATED APOPTOSIS-INDUCING LIGAND COMPND 5 RECEPTOR 2,TRAIL RECEPTOR 2,TRAIL-R2; 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: TNFRSF10B, DR5, KILLER, TRAILR2, TRICK2, ZTNFR9, SOURCE 6 UNQ160/PRO186; SOURCE 7 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: X-33 KEYWDS PRELIGAND ASSOCIATION STRUCTURE, AUTOINHIBITION STATE, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR G.DU,L.ZHAO,J.J.CHOU REVDAT 1 15-FEB-23 8DPX 0 JRNL AUTH G.DU,L.ZHAO,Y.ZHENG,A.BELFETMI,T.CAI,B.XU,K.HEYNINCK, JRNL AUTH 2 K.VAN DEN HEEDE,M.A.BUYSE,P.FONTANA,M.BOWMAN,L.L.LIN,H.WU, JRNL AUTH 3 J.J.CHOU JRNL TITL AUTOINHIBITORY STRUCTURE OF PRELIGAND ASSOCIATION STATE JRNL TITL 2 IMPLICATES A NEW STRATEGY TO ATTAIN EFFECTIVE DR5 RECEPTOR JRNL TITL 3 ACTIVATION. JRNL REF CELL RES. V. 33 131 2023 JRNL REFN ISSN 1001-0602 JRNL PMID 36604598 JRNL DOI 10.1038/S41422-022-00755-2 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8DPX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267141. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM [U-100% 15N, U-100% 13C, REMARK 210 U-85% 2H] DR5 ECTODOMAIN, 4.4 MM REMARK 210 DGS-NTA (NI), 44 MM DMPC, 88 MM REMARK 210 D7PC, 95% H2O/5% D2O; 500 UM [U- REMARK 210 100% 15N; U-100% 2H] DR5 REMARK 210 ECTODOMAIN, 5.5 MM DGS-NTA (NI), REMARK 210 55 MM DMPC, 110 MM D7PC, 95% H2O/ REMARK 210 5% D2O; 250 UM [U-100% 15N; U- REMARK 210 100% 2H] ISOTOPICALLY MIXED DR5 REMARK 210 ECTODOMAIN, 250 UM [U-100% 13C] REMARK 210 DR5 ECTODOMAIN, 5.5 MM DGS-NTA REMARK 210 (NI), 55 MM DMPC, 110 MM D7PC, REMARK 210 95% H2O/5% D2O; 250 UM [U-100% REMARK 210 13C; U-100% 15N; U-95% 2H] REMARK 210 ISOTOPICALLY MIXED DR5 REMARK 210 ECTODOMAIN, 250 UM DR5 REMARK 210 ECTODOMAIN, 5.5 MM DGS-NTA (NI), REMARK 210 55 MM DMPC, 110 MM D7PC, 95% H2O/ REMARK 210 5% D2O; 500 UM [U-100% 13C; U- REMARK 210 100% 15N] DR5 ECTODOMAIN, 5.5 MM REMARK 210 DGS-NTA (NI), 55 MM DMPC, 110 MM REMARK 210 D7PC, 95% H2O/5% D2O; 400 UM [U- REMARK 210 100% 15N, U-85% 2H] DR5 REMARK 210 ECTODOMAIN, 4.4 MM DGS-NTA (NI), REMARK 210 44 MM DMPC, 88 MM D7PC, 95% H2O/ REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY-HSQC; 3D HNCA; REMARK 210 3D HN(CO)CA; 3D HN(CA)CO; 3D REMARK 210 HNCO; 3D HNCACB; 3D HN(COCA)CB; REMARK 210 3D 1H-15N NOESY-TROSY; 13C- REMARK 210 FILTERED 1H-15N NOESY-TROSY; 2D REMARK 210 1H-13C HSQC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, XEASY, CCPNMR ANALYSIS REMARK 210 VERSION 2, TALOS+ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-15 REMARK 470 RES CSSEQI ATOMS REMARK 470 ASP A 185 O REMARK 470 ASP B 185 O REMARK 470 ASP C 185 O 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 1 GLU A 151 41.46 38.78 REMARK 500 1 CYS A 160 150.30 -46.13 REMARK 500 1 VAL A 167 -13.12 -154.41 REMARK 500 1 LYS A 181 -62.85 -147.88 REMARK 500 1 SER A 183 81.43 -178.73 REMARK 500 1 ASP B 109 56.43 -142.06 REMARK 500 1 PRO B 161 170.00 -48.68 REMARK 500 1 VAL B 167 -5.94 -140.50 REMARK 500 1 ASP C 102 168.20 174.37 REMARK 500 1 GLU C 151 21.76 -168.34 REMARK 500 1 PRO C 161 163.44 -47.64 REMARK 500 1 VAL C 167 -19.32 -152.21 REMARK 500 1 LYS C 181 96.05 46.81 REMARK 500 2 GLU A 78 69.40 -117.88 REMARK 500 2 ASP A 109 50.53 -117.86 REMARK 500 2 GLU A 151 50.29 -175.42 REMARK 500 2 VAL A 167 -15.48 -153.02 REMARK 500 2 LYS A 181 134.02 -172.92 REMARK 500 2 SER A 183 29.73 -146.16 REMARK 500 2 GLU B 151 22.52 46.38 REMARK 500 2 PRO B 161 170.55 -53.82 REMARK 500 2 VAL B 167 -1.51 -151.50 REMARK 500 2 LYS B 181 -61.18 -152.58 REMARK 500 2 GLU B 182 145.92 -173.65 REMARK 500 2 SER B 183 29.58 -166.12 REMARK 500 2 GLU C 151 38.24 -172.91 REMARK 500 2 VAL C 167 -22.55 -143.02 REMARK 500 2 LYS C 181 104.07 56.93 REMARK 500 2 SER C 183 -54.00 -173.92 REMARK 500 3 PRO A 150 -154.80 -65.83 REMARK 500 3 GLU A 151 24.15 -77.43 REMARK 500 3 VAL A 167 -20.14 -154.88 REMARK 500 3 LYS A 181 -43.15 -151.85 REMARK 500 3 SER A 183 -49.53 -167.02 REMARK 500 3 ASP B 102 163.39 177.73 REMARK 500 3 GLU B 151 25.97 44.18 REMARK 500 3 PRO B 161 171.01 -59.81 REMARK 500 3 VAL B 167 -3.38 -148.20 REMARK 500 3 LYS B 181 -66.99 -132.67 REMARK 500 3 GLU B 182 131.50 -177.86 REMARK 500 3 PRO C 150 -169.00 -54.75 REMARK 500 3 PRO C 161 167.62 -48.39 REMARK 500 3 VAL C 167 -11.90 -157.96 REMARK 500 3 LYS C 181 128.62 63.68 REMARK 500 3 SER C 183 -72.35 65.62 REMARK 500 4 GLU A 78 171.39 -54.50 REMARK 500 4 ASP A 109 51.78 -119.61 REMARK 500 4 GLU A 151 32.88 -144.38 REMARK 500 4 CYS A 160 152.35 -45.63 REMARK 500 4 VAL A 167 -26.83 -148.06 REMARK 500 REMARK 500 THIS ENTRY HAS 229 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31034 RELATED DB: BMRB REMARK 900 PRELIGAND ASSOCIATION STRUCTURE OF DR5 DBREF 8DPX A 77 184 UNP O14763 TR10B_HUMAN 77 184 DBREF 8DPX B 77 184 UNP O14763 TR10B_HUMAN 77 184 DBREF 8DPX C 77 184 UNP O14763 TR10B_HUMAN 77 184 SEQADV 8DPX ASP A 185 UNP O14763 EXPRESSION TAG SEQADV 8DPX ASP B 185 UNP O14763 EXPRESSION TAG SEQADV 8DPX ASP C 185 UNP O14763 EXPRESSION TAG SEQRES 1 A 109 SER GLU GLY LEU CYS PRO PRO GLY HIS HIS ILE SER GLU SEQRES 2 A 109 ASP GLY ARG ASP CYS ILE SER CYS LYS TYR GLY GLN ASP SEQRES 3 A 109 TYR SER THR HIS TRP ASN ASP LEU LEU PHE CYS LEU ARG SEQRES 4 A 109 CYS THR ARG CYS ASP SER GLY GLU VAL GLU LEU SER PRO SEQRES 5 A 109 CYS THR THR THR ARG ASN THR VAL CYS GLN CYS GLU GLU SEQRES 6 A 109 GLY THR PHE ARG GLU GLU ASP SER PRO GLU MET CYS ARG SEQRES 7 A 109 LYS CYS ARG THR GLY CYS PRO ARG GLY MET VAL LYS VAL SEQRES 8 A 109 GLY ASP CYS THR PRO TRP SER ASP ILE GLU CYS VAL HIS SEQRES 9 A 109 LYS GLU SER GLY ASP SEQRES 1 B 109 SER GLU GLY LEU CYS PRO PRO GLY HIS HIS ILE SER GLU SEQRES 2 B 109 ASP GLY ARG ASP CYS ILE SER CYS LYS TYR GLY GLN ASP SEQRES 3 B 109 TYR SER THR HIS TRP ASN ASP LEU LEU PHE CYS LEU ARG SEQRES 4 B 109 CYS THR ARG CYS ASP SER GLY GLU VAL GLU LEU SER PRO SEQRES 5 B 109 CYS THR THR THR ARG ASN THR VAL CYS GLN CYS GLU GLU SEQRES 6 B 109 GLY THR PHE ARG GLU GLU ASP SER PRO GLU MET CYS ARG SEQRES 7 B 109 LYS CYS ARG THR GLY CYS PRO ARG GLY MET VAL LYS VAL SEQRES 8 B 109 GLY ASP CYS THR PRO TRP SER ASP ILE GLU CYS VAL HIS SEQRES 9 B 109 LYS GLU SER GLY ASP SEQRES 1 C 109 SER GLU GLY LEU CYS PRO PRO GLY HIS HIS ILE SER GLU SEQRES 2 C 109 ASP GLY ARG ASP CYS ILE SER CYS LYS TYR GLY GLN ASP SEQRES 3 C 109 TYR SER THR HIS TRP ASN ASP LEU LEU PHE CYS LEU ARG SEQRES 4 C 109 CYS THR ARG CYS ASP SER GLY GLU VAL GLU LEU SER PRO SEQRES 5 C 109 CYS THR THR THR ARG ASN THR VAL CYS GLN CYS GLU GLU SEQRES 6 C 109 GLY THR PHE ARG GLU GLU ASP SER PRO GLU MET CYS ARG SEQRES 7 C 109 LYS CYS ARG THR GLY CYS PRO ARG GLY MET VAL LYS VAL SEQRES 8 C 109 GLY ASP CYS THR PRO TRP SER ASP ILE GLU CYS VAL HIS SEQRES 9 C 109 LYS GLU SER GLY ASP SHEET 1 AA1 2 HIS A 85 ILE A 87 0 SHEET 2 AA1 2 CYS A 94 SER A 96 -1 O ILE A 95 N HIS A 86 SHEET 1 AA2 2 GLU A 123 GLU A 125 0 SHEET 2 AA2 2 CYS A 137 CYS A 139 -1 O GLN A 138 N VAL A 124 SHEET 1 AA3 2 THR A 143 PHE A 144 0 SHEET 2 AA3 2 ARG A 154 LYS A 155 -1 O ARG A 154 N PHE A 144 SHEET 1 AA4 2 MET A 164 LYS A 166 0 SHEET 2 AA4 2 CYS A 178 HIS A 180 -1 O VAL A 179 N VAL A 165 SHEET 1 AA5 2 HIS B 85 ILE B 87 0 SHEET 2 AA5 2 CYS B 94 SER B 96 -1 O ILE B 95 N HIS B 86 SHEET 1 AA6 2 ASP B 102 TYR B 103 0 SHEET 2 AA6 2 LEU B 114 ARG B 115 -1 O LEU B 114 N TYR B 103 SHEET 1 AA7 2 GLU B 123 SER B 127 0 SHEET 2 AA7 2 VAL B 136 CYS B 139 -1 O GLN B 138 N VAL B 124 SHEET 1 AA8 2 THR B 143 PHE B 144 0 SHEET 2 AA8 2 ARG B 154 LYS B 155 -1 O ARG B 154 N PHE B 144 SHEET 1 AA9 2 MET B 164 LYS B 166 0 SHEET 2 AA9 2 CYS B 178 HIS B 180 -1 O VAL B 179 N VAL B 165 SHEET 1 AB1 2 HIS C 85 ILE C 87 0 SHEET 2 AB1 2 CYS C 94 SER C 96 -1 O ILE C 95 N HIS C 86 SHEET 1 AB2 2 GLU C 123 SER C 127 0 SHEET 2 AB2 2 VAL C 136 CYS C 139 -1 O GLN C 138 N VAL C 124 SHEET 1 AB3 2 THR C 143 PHE C 144 0 SHEET 2 AB3 2 ARG C 154 LYS C 155 -1 O ARG C 154 N PHE C 144 SHEET 1 AB4 2 VAL C 165 GLY C 168 0 SHEET 2 AB4 2 GLU C 177 VAL C 179 -1 O VAL C 179 N VAL C 165 SSBOND 1 CYS A 81 CYS A 94 1555 1555 2.02 SSBOND 2 CYS A 97 CYS A 113 1555 1555 2.03 SSBOND 3 CYS A 116 CYS A 129 1555 1555 2.02 SSBOND 4 CYS A 119 CYS A 137 1555 1555 2.02 SSBOND 5 CYS A 139 CYS A 153 1555 1555 2.02 SSBOND 6 CYS A 156 CYS A 170 1555 1555 2.02 SSBOND 7 CYS A 160 CYS A 178 1555 1555 2.02 SSBOND 8 CYS B 81 CYS B 94 1555 1555 2.02 SSBOND 9 CYS B 97 CYS B 113 1555 1555 2.03 SSBOND 10 CYS B 116 CYS B 129 1555 1555 2.02 SSBOND 11 CYS B 119 CYS B 137 1555 1555 2.03 SSBOND 12 CYS B 139 CYS B 153 1555 1555 2.02 SSBOND 13 CYS B 156 CYS B 170 1555 1555 2.02 SSBOND 14 CYS B 160 CYS B 178 1555 1555 2.02 SSBOND 15 CYS C 81 CYS C 94 1555 1555 2.02 SSBOND 16 CYS C 97 CYS C 113 1555 1555 2.03 SSBOND 17 CYS C 116 CYS C 129 1555 1555 2.02 SSBOND 18 CYS C 119 CYS C 137 1555 1555 2.02 SSBOND 19 CYS C 139 CYS C 153 1555 1555 2.03 SSBOND 20 CYS C 156 CYS C 170 1555 1555 2.03 SSBOND 21 CYS C 160 CYS C 178 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1