PDB Short entry for 6NHW HEADER IMMUNE SYSTEM 24-DEC-18 6NHW TITLE STRUCTURE OF THE TRANSMEMBRANE DOMAIN OF THE DEATH RECEPTOR 5 - DIMER TITLE 2 OF TRIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 10B; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 FRAGMENT: RESIDUES 208-242; COMPND 5 SYNONYM: DEATH RECEPTOR 5,TNF-RELATED APOPTOSIS-INDUCING LIGAND COMPND 6 RECEPTOR 2,TRAIL-R2; COMPND 7 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: 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 DEATH RECEPTOR 5, TRANSMEMBRANE HELIX OLIGOMER, TRANSMEMBRANE HELIX KEYWDS 2 MEDIATED SIGNALING, PRELIGAND AUTOINHIBITION, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR J.J.CHOU,L.PAN,Q.FU,L.ZHAO,W.CHEN,A.PIAI,T.FU,H.WU REVDAT 4 14-JUN-23 6NHW 1 REMARK REVDAT 3 01-JAN-20 6NHW 1 REMARK REVDAT 2 20-MAR-19 6NHW 1 JRNL REVDAT 1 27-FEB-19 6NHW 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 3.851 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6NHW 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_1000238765. 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 DEATH REMARK 210 RECEPTOR 5, 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 REMARK 210 DEATH RECEPTOR 5, 50 MM [ACYL REMARK 210 CHAIN U-2H] DMPC, 100 MM [ACYL REMARK 210 CHAIN U-2H] DHPC, 20 MM SODIUM REMARK 210 PHOSPHATE, 95% H2O/5% D2O; 0.4 REMARK 210 MM [U-15N; U-2H; 15%-13C] REMARK 210 TRANSMEMBRANE DOMAIN OF DEATH REMARK 210 RECEPTOR 5, 50 MM [ACYL CHAIN U- REMARK 210 2H] DMPC, 100 MM [ACYL CHAIN U- REMARK 210 2H] DHPC, 20 MM SODIUM PHOSPHATE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TROSY-HSQC; TROSY-HNCA; TROSY REMARK 210 -HNCOCA; TROSY-HNCACO; 3D 15N REMARK 210 NOE-TROSY-HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 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 : NMRPIPE, CCPNMR, XEASY, X-PLOR REMARK 210 NIH 3.851 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 LYS A 238 88.99 -168.00 REMARK 500 1 LYS A 239 -164.21 71.92 REMARK 500 1 SER B 210 5.92 -167.53 REMARK 500 1 TRP B 237 67.56 -155.36 REMARK 500 1 TRP C 237 -76.49 -64.26 REMARK 500 1 LYS C 238 -135.61 55.80 REMARK 500 1 LYS C 239 78.56 57.21 REMARK 500 1 LYS D 239 177.25 64.10 REMARK 500 1 SER E 210 17.26 -161.18 REMARK 500 1 TRP E 237 25.79 -77.70 REMARK 500 1 SER F 210 88.66 -167.91 REMARK 500 1 LYS F 238 82.69 -62.94 REMARK 500 2 TRP A 237 -141.42 -78.39 REMARK 500 2 LYS A 239 118.86 -160.12 REMARK 500 2 PRO B 208 -110.66 -80.54 REMARK 500 2 TRP B 237 -18.35 -157.42 REMARK 500 2 LYS B 238 -40.17 66.62 REMARK 500 2 SER C 210 -57.10 -165.60 REMARK 500 2 TRP C 237 -124.82 -71.42 REMARK 500 2 LYS C 238 111.39 54.67 REMARK 500 2 LYS D 239 -157.65 59.71 REMARK 500 2 SER E 210 -111.04 -165.95 REMARK 500 2 LYS E 239 93.17 -68.55 REMARK 500 3 SER A 210 27.65 -162.61 REMARK 500 3 LYS A 238 173.57 -52.37 REMARK 500 3 SER B 210 -57.59 -165.67 REMARK 500 3 TRP B 237 160.80 61.50 REMARK 500 3 LYS B 238 -121.82 -129.49 REMARK 500 3 LYS C 238 26.07 -162.99 REMARK 500 3 SER E 210 -78.20 -64.26 REMARK 500 3 LYS E 238 -101.61 -59.62 REMARK 500 3 PRO F 208 -178.48 -52.37 REMARK 500 3 SER F 210 -1.13 -163.63 REMARK 500 3 LYS F 238 -21.66 -147.13 REMARK 500 4 SER A 210 -27.27 -168.38 REMARK 500 4 SER B 210 -25.54 -167.22 REMARK 500 4 LYS B 238 -102.78 -67.21 REMARK 500 4 LYS B 239 108.37 58.28 REMARK 500 4 LYS C 238 -18.78 -152.59 REMARK 500 4 LYS C 239 -167.80 -65.99 REMARK 500 4 PRO D 208 168.94 -49.12 REMARK 500 4 SER E 210 54.60 -163.26 REMARK 500 4 TRP E 237 8.87 51.27 REMARK 500 4 PRO F 208 38.29 -76.42 REMARK 500 4 LYS F 238 23.59 -172.34 REMARK 500 5 SER B 210 -97.05 55.68 REMARK 500 5 TRP B 237 61.31 -101.86 REMARK 500 5 LYS B 238 72.56 -63.26 REMARK 500 5 PRO C 208 -162.99 -57.93 REMARK 500 5 SER C 210 113.80 56.85 REMARK 500 REMARK 500 THIS ENTRY HAS 171 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30553 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE TRANSMEMBRANE DOMAIN OF THE DEATH RECEPTOR 5 - REMARK 900 DIMER OF TRIMER DBREF 6NHW A 208 242 UNP O14763 TR10B_HUMAN 208 242 DBREF 6NHW B 208 242 UNP O14763 TR10B_HUMAN 208 242 DBREF 6NHW C 208 242 UNP O14763 TR10B_HUMAN 208 242 DBREF 6NHW D 208 242 UNP O14763 TR10B_HUMAN 208 242 DBREF 6NHW E 208 242 UNP O14763 TR10B_HUMAN 208 242 DBREF 6NHW F 208 242 UNP O14763 TR10B_HUMAN 208 242 SEQADV 6NHW MET A 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHW GLY A 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHW MET B 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHW GLY B 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHW MET C 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHW GLY C 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHW MET D 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHW GLY D 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHW MET E 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHW GLY E 209 UNP O14763 CYS 209 CONFLICT SEQADV 6NHW MET F 207 UNP O14763 INITIATING METHIONINE SEQADV 6NHW GLY F 209 UNP O14763 CYS 209 CONFLICT SEQRES 1 A 36 MET PRO GLY SER LEU SER GLY ILE ILE ILE GLY 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 GLY 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 GLY 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 SEQRES 1 D 36 MET PRO GLY SER LEU SER GLY ILE ILE ILE GLY VAL THR SEQRES 2 D 36 VAL ALA ALA VAL VAL LEU ILE VAL ALA VAL PHE VAL CYS SEQRES 3 D 36 LYS SER LEU LEU TRP LYS LYS VAL LEU PRO SEQRES 1 E 36 MET PRO GLY SER LEU SER GLY ILE ILE ILE GLY VAL THR SEQRES 2 E 36 VAL ALA ALA VAL VAL LEU ILE VAL ALA VAL PHE VAL CYS SEQRES 3 E 36 LYS SER LEU LEU TRP LYS LYS VAL LEU PRO SEQRES 1 F 36 MET PRO GLY SER LEU SER GLY ILE ILE ILE GLY VAL THR SEQRES 2 F 36 VAL ALA ALA VAL VAL LEU ILE VAL ALA VAL PHE VAL CYS SEQRES 3 F 36 LYS SER LEU LEU TRP LYS LYS VAL LEU PRO HELIX 1 AA1 SER A 210 SER A 212 5 3 HELIX 2 AA2 GLY A 213 TRP A 237 1 25 HELIX 3 AA3 SER B 210 SER B 212 5 3 HELIX 4 AA4 GLY B 213 LEU B 235 1 23 HELIX 5 AA5 SER C 210 GLY C 213 5 4 HELIX 6 AA6 ILE C 214 LEU C 235 1 22 HELIX 7 AA7 SER D 210 TRP D 237 1 28 HELIX 8 AA8 SER E 210 LYS E 233 1 24 HELIX 9 AA9 SER F 210 LEU F 235 1 26 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