HEADER IMMUNE SYSTEM 24-DEC-18 6NHY TITLE STRUCTURE OF THE TRANSMEMBRANE DOMAIN OF THE DEATH RECEPTOR 5 MUTANT TITLE 2 (G217Y) - TRIMER ONLY 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-R2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: 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: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PMM-LR6 KEYWDS TRANSMEMBRANE HELIX TRIMER, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR J.J.CHOU,L.PAN,L.ZHAO,W.CHEN,A.PIAI,T.FU,H.WU,Z.LIU REVDAT 4 14-JUN-23 6NHY 1 REMARK REVDAT 3 01-JAN-20 6NHY 1 REMARK REVDAT 2 20-MAR-19 6NHY 1 JRNL REVDAT 1 27-FEB-19 6NHY 0 JRNL AUTH L.PAN,T.M.FU,W.ZHAO,L.ZHAO,W.CHEN,C.QIU,W.LIU,Z.LIU,A.PIAI, JRNL AUTH 2 Q.FU,S.CHEN,H.WU,J.J.CHOU JRNL TITL HIGHER-ORDER CLUSTERING OF THE TRANSMEMBRANE ANCHOR OF DR5 JRNL TITL 2 DRIVES SIGNALING. JRNL REF CELL V. 176 1477 2019 JRNL REFN ISSN 1097-4172 JRNL PMID 30827683 JRNL DOI 10.1016/J.CELL.2019.02.001 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 6NHY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000238767. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-13C; U-15N; 85%-2H] REMARK 210 TRANSMEMBRANE DOMAIN OF DR5 REMARK 210 MUTANT G217Y, 50 MM DMPC, 100 MM REMARK 210 DHPC, 20 MM SODIUM PHOSPHATE, 95% REMARK 210 H2O/5% D2O; 0.8 MM [U-13C; U- REMARK 210 15N] TRANSMEMBRANE DOMAIN OF DR5 REMARK 210 MUTANT G217Y, 50 MM [ACYL CHAIN REMARK 210 U-2H] DMPC, 100 MM [ACYL CHAIN U- REMARK 210 2H] DHPC, 20 MM SODIUM PHOSPHATE, REMARK 210 95% H2O/5% D2O; 0.4 MM [15%-13C; REMARK 210 U-15N; H-2H] TRANSMEMBRANE REMARK 210 DOMAIN OF DR5 MUTANT G217Y, 50 REMARK 210 MM [ACYL CHAIN U-2H] DMPC, 100 REMARK 210 MM [ACYL CHAIN U-2H] DHPC, 20 MM REMARK 210 SODIUM PHOSPHATE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TROSY HSQC; TROSY HNCA; TROSY REMARK 210 HNCOCA; TROSY HNCACO; 3D 15N NOE- REMARK 210 TROSY-HSQC; 2D 1H-13C HSQC; 3D REMARK 210 13C NOE-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, XEASY, NMRPIPE, REMARK 210 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 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 SER A 210 35.63 -166.46 REMARK 500 1 LYS A 239 -9.54 -53.17 REMARK 500 1 PRO B 208 -76.95 -59.74 REMARK 500 1 SER B 210 21.03 -158.90 REMARK 500 1 PRO C 208 42.03 -76.31 REMARK 500 1 SER C 210 71.14 -167.77 REMARK 500 2 PRO A 208 -167.55 -72.96 REMARK 500 2 LEU A 211 -37.71 -159.98 REMARK 500 2 LYS A 239 -18.12 74.19 REMARK 500 2 SER B 210 149.23 61.62 REMARK 500 2 LEU B 211 30.23 -170.55 REMARK 500 2 LYS B 239 -52.30 -146.02 REMARK 500 2 SER C 210 45.10 -166.76 REMARK 500 2 LYS C 239 -67.99 -158.37 REMARK 500 3 PRO A 208 -166.17 -72.59 REMARK 500 3 SER A 210 89.75 -56.62 REMARK 500 3 LYS A 239 -34.64 -167.12 REMARK 500 3 LEU C 211 -45.58 -166.48 REMARK 500 3 LYS C 238 -53.66 -132.36 REMARK 500 3 LYS C 239 -19.86 65.21 REMARK 500 4 SER A 210 80.31 -167.93 REMARK 500 4 LEU A 211 -0.83 -161.63 REMARK 500 4 SER B 210 37.63 -163.56 REMARK 500 4 LEU B 211 9.07 54.70 REMARK 500 5 SER A 210 58.51 -169.56 REMARK 500 5 LEU A 211 -9.91 -145.51 REMARK 500 5 SER B 210 121.99 59.06 REMARK 500 5 LEU B 211 -49.13 -165.39 REMARK 500 5 LYS B 239 -7.87 72.33 REMARK 500 5 SER C 210 174.18 56.92 REMARK 500 5 LEU C 211 -33.56 76.23 REMARK 500 5 LYS C 239 9.77 82.44 REMARK 500 6 LEU A 211 -0.37 65.31 REMARK 500 6 SER B 210 76.75 -166.73 REMARK 500 6 LYS C 238 36.58 33.70 REMARK 500 6 LYS C 239 -7.37 70.52 REMARK 500 7 SER A 210 167.12 58.19 REMARK 500 7 LYS A 239 -8.68 71.72 REMARK 500 7 LEU B 211 -36.98 82.70 REMARK 500 8 LEU A 211 -48.31 -163.08 REMARK 500 8 LEU B 211 23.74 -152.27 REMARK 500 8 LYS B 238 -56.90 -136.74 REMARK 500 8 LYS B 239 -2.74 71.25 REMARK 500 8 LEU C 211 46.48 -170.37 REMARK 500 9 LEU A 211 9.14 56.94 REMARK 500 9 LYS A 239 -17.70 92.07 REMARK 500 9 SER B 210 72.32 -67.28 REMARK 500 9 LEU B 211 -51.31 -162.60 REMARK 500 9 LEU C 211 -51.27 -165.12 REMARK 500 9 LYS C 238 -62.77 -139.93 REMARK 500 REMARK 500 THIS ENTRY HAS 80 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30554 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE TRANSMEMBRANE DOMAIN OF THE DEATH RECEPTOR 5 REMARK 900 MUTANT (G217Y) - TRIMER ONLY DBREF 6NHY A 208 242 UNP O14763 TR10B_HUMAN 208 242 DBREF 6NHY B 208 242 UNP O14763 TR10B_HUMAN 208 242 DBREF 6NHY C 208 242 UNP O14763 TR10B_HUMAN 208 242 SEQADV 6NHY MET A 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHY GLY A 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHY TYR A 217 UNP O14763 GLY 217 ENGINEERED MUTATION SEQADV 6NHY MET B 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHY GLY B 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHY TYR B 217 UNP O14763 GLY 217 ENGINEERED MUTATION SEQADV 6NHY MET C 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHY GLY C 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHY TYR C 217 UNP O14763 GLY 217 ENGINEERED MUTATION SEQRES 1 A 36 MET PRO GLY SER LEU SER GLY ILE ILE ILE TYR VAL THR SEQRES 2 A 36 VAL ALA ALA VAL VAL LEU ILE VAL ALA VAL PHE VAL CYS SEQRES 3 A 36 LYS SER LEU LEU TRP LYS LYS VAL LEU PRO SEQRES 1 B 36 MET PRO GLY SER LEU SER GLY ILE ILE ILE TYR VAL THR SEQRES 2 B 36 VAL ALA ALA VAL VAL LEU ILE VAL ALA VAL PHE VAL CYS SEQRES 3 B 36 LYS SER LEU LEU TRP LYS LYS VAL LEU PRO SEQRES 1 C 36 MET PRO GLY SER LEU SER GLY ILE ILE ILE TYR VAL THR SEQRES 2 C 36 VAL ALA ALA VAL VAL LEU ILE VAL ALA VAL PHE VAL CYS SEQRES 3 C 36 LYS SER LEU LEU TRP LYS LYS VAL LEU PRO HELIX 1 AA1 SER A 210 TRP A 237 1 28 HELIX 2 AA2 LEU B 211 TRP B 237 1 27 HELIX 3 AA3 SER C 210 LYS C 238 1 29 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