HEADER RECEPTOR 28-JAN-97 1NGR TITLE DEATH DOMAIN OF P75 LOW AFFINITY NEUROTROPHIN RECEPTOR, RESIDUES 334- TITLE 2 418, NMR, 20 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: P75 LOW AFFINITY NEUROTROPHIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DEATH DOMAIN, RESIDUES 281 - 425; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 CELL: NERVE CELLS; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: M15-(PREP4); SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE31 KEYWDS RECEPTOR, P75, INTRACELLULAR DOMAIN, NEUROTROPHIN RECEPTOR, DEATH KEYWDS 2 DOMAIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.OTTING,E.LIEPINSH REVDAT 3 23-FEB-22 1NGR 1 REMARK REVDAT 2 24-FEB-09 1NGR 1 VERSN REVDAT 1 29-JUL-97 1NGR 0 JRNL AUTH E.LIEPINSH,L.L.ILAG,G.OTTING,C.F.IBANEZ JRNL TITL NMR STRUCTURE OF THE DEATH DOMAIN OF THE P75 NEUROTROPHIN JRNL TITL 2 RECEPTOR. JRNL REF EMBO J. V. 16 4999 1997 JRNL REFN ISSN 0261-4189 JRNL PMID 9305641 JRNL DOI 10.1093/EMBOJ/16.16.4999 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL REMARK 3 AUTHORS : LUGINBUHL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DIANA MINIMIZATION TO TARGET FUNCTION REMARK 3 LESS THAN 1, RESTRAINED ENERGY MINIMIZATION USING OPAL REMARK 4 REMARK 4 1NGR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175285. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; COSY; TOCSY; 3D NOESY-15N REMARK 210 -HSQC; 3D TOCSY-HSQC; 3D HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX800; DMX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : EASY, HABAS, DIANA, OPAL REMARK 210 METHOD USED : VARIABLE TARGET FUNCTION (DIANA) REMARK 210 APPROACH REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TARGET FUNCTION AFTER REMARK 210 DIANA REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: DISTANCE CONSTRAINTS FROM 3D NOESY-15N-HSQC AND 2D NOESY, REMARK 210 COUPLING CONSTANTS FROM 3D HNHA-EXPERIMENT, 2QF-COSY, AND 15N- REMARK 210 HSQC. A 15N-LABELED SAMPLE OF P75ICD WAS USED. CONSTRAINTS USED: REMARK 210 914 UPPER DISTANCE LIMITS FROM NOE DATA 154 COUPLING CONSTANTS REMARK 210 CONSTRAINING DIHEDRAL ANGLES IONIC_STRENGTH: NO SALT ADDED REMARK 210 PRESSURE: 1 ATM SOLVENT SYSTEM: 90% H2O/10% D2O 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 ARG A 345 CD - NE - CZ ANGL. DEV. = 11.4 DEGREES REMARK 500 2 ARG A 345 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 2 GLU A 413 CB - CA - C ANGL. DEV. = 17.2 DEGREES REMARK 500 4 GLU A 413 CB - CA - C ANGL. DEV. = 13.6 DEGREES REMARK 500 5 TYR A 337 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 6 TYR A 337 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 10 GLU A 413 CB - CA - C ANGL. DEV. = 15.3 DEGREES REMARK 500 12 TYR A 337 CB - CG - CD2 ANGL. DEV. = -5.1 DEGREES REMARK 500 13 ARG A 408 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 14 ARG A 404 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 TYR A 337 CB - CG - CD2 ANGL. DEV. = -4.5 DEGREES REMARK 500 17 TYR A 337 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 17 GLU A 413 CB - CA - C ANGL. DEV. = 14.5 DEGREES REMARK 500 19 GLU A 413 CB - CA - C ANGL. DEV. = 15.5 DEGREES 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 1 SER A 338 -7.58 -59.81 REMARK 500 1 THR A 343 -12.28 -48.36 REMARK 500 1 ASP A 355 -71.48 178.13 REMARK 500 1 PRO A 380 -80.25 -54.73 REMARK 500 1 GLN A 407 19.13 44.18 REMARK 500 1 SER A 417 -61.27 -158.22 REMARK 500 2 LEU A 342 -105.42 -147.46 REMARK 500 2 THR A 343 -38.18 -28.67 REMARK 500 2 LEU A 352 59.49 -69.92 REMARK 500 2 ASP A 355 -61.24 -165.06 REMARK 500 2 PRO A 380 -74.55 -53.26 REMARK 500 2 SER A 393 -19.08 -170.39 REMARK 500 2 GLN A 407 18.90 54.53 REMARK 500 2 SER A 417 -61.10 -149.86 REMARK 500 3 LEU A 336 -179.25 -61.87 REMARK 500 3 THR A 343 -9.88 -48.61 REMARK 500 3 ASP A 355 -59.06 177.79 REMARK 500 3 PRO A 380 -83.44 -55.75 REMARK 500 3 SER A 393 -29.79 148.40 REMARK 500 3 GLN A 407 19.06 52.94 REMARK 500 3 SER A 417 -61.12 137.27 REMARK 500 4 PRO A 380 -87.34 -58.04 REMARK 500 4 ASP A 392 102.13 -49.31 REMARK 500 4 ALA A 394 57.94 -66.70 REMARK 500 4 GLN A 407 19.13 48.81 REMARK 500 4 SER A 417 -28.12 59.00 REMARK 500 5 LEU A 342 -86.68 -148.24 REMARK 500 5 THR A 343 -51.96 -29.15 REMARK 500 5 ASN A 353 144.67 -37.76 REMARK 500 5 ASP A 355 -43.55 169.62 REMARK 500 5 PRO A 380 -74.68 -53.76 REMARK 500 5 ASP A 392 102.14 -56.00 REMARK 500 5 ALA A 394 48.63 -69.39 REMARK 500 5 GLN A 407 27.85 49.89 REMARK 500 5 SER A 417 -61.93 -126.82 REMARK 500 6 TYR A 337 -60.28 -95.86 REMARK 500 6 THR A 343 -8.07 -55.58 REMARK 500 6 ASP A 355 -67.06 177.73 REMARK 500 6 PRO A 380 -71.29 -52.22 REMARK 500 6 SER A 393 -5.31 134.89 REMARK 500 6 ALA A 394 57.15 -68.79 REMARK 500 6 GLN A 407 19.04 55.94 REMARK 500 6 SER A 417 -62.21 58.01 REMARK 500 7 ASP A 355 -70.92 174.29 REMARK 500 7 PRO A 380 -80.16 -57.32 REMARK 500 7 SER A 417 -51.31 -158.72 REMARK 500 8 THR A 343 -13.96 -47.82 REMARK 500 8 LEU A 352 55.73 -69.66 REMARK 500 8 ASP A 355 -64.64 -175.07 REMARK 500 8 PRO A 380 -79.04 -56.06 REMARK 500 REMARK 500 THIS ENTRY HAS 138 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 382 0.09 SIDE CHAIN REMARK 500 2 TYR A 337 0.09 SIDE CHAIN REMARK 500 3 ARG A 408 0.10 SIDE CHAIN REMARK 500 4 ARG A 382 0.10 SIDE CHAIN REMARK 500 4 ARG A 405 0.08 SIDE CHAIN REMARK 500 5 ARG A 408 0.11 SIDE CHAIN REMARK 500 6 ARG A 345 0.08 SIDE CHAIN REMARK 500 6 TYR A 366 0.09 SIDE CHAIN REMARK 500 6 ARG A 408 0.09 SIDE CHAIN REMARK 500 7 ARG A 345 0.11 SIDE CHAIN REMARK 500 7 ARG A 405 0.14 SIDE CHAIN REMARK 500 8 ARG A 382 0.11 SIDE CHAIN REMARK 500 9 TYR A 337 0.06 SIDE CHAIN REMARK 500 9 TYR A 366 0.07 SIDE CHAIN REMARK 500 10 TYR A 366 0.07 SIDE CHAIN REMARK 500 10 ARG A 382 0.12 SIDE CHAIN REMARK 500 10 ARG A 405 0.14 SIDE CHAIN REMARK 500 11 TYR A 337 0.11 SIDE CHAIN REMARK 500 11 TYR A 366 0.07 SIDE CHAIN REMARK 500 11 ARG A 382 0.08 SIDE CHAIN REMARK 500 11 ARG A 405 0.15 SIDE CHAIN REMARK 500 12 ARG A 408 0.09 SIDE CHAIN REMARK 500 13 TYR A 366 0.07 SIDE CHAIN REMARK 500 13 ARG A 382 0.08 SIDE CHAIN REMARK 500 13 ARG A 404 0.10 SIDE CHAIN REMARK 500 15 TYR A 337 0.07 SIDE CHAIN REMARK 500 15 TYR A 366 0.07 SIDE CHAIN REMARK 500 15 ARG A 382 0.10 SIDE CHAIN REMARK 500 16 ARG A 345 0.08 SIDE CHAIN REMARK 500 16 ARG A 382 0.09 SIDE CHAIN REMARK 500 17 TYR A 337 0.08 SIDE CHAIN REMARK 500 17 ARG A 345 0.08 SIDE CHAIN REMARK 500 17 TYR A 366 0.07 SIDE CHAIN REMARK 500 18 TYR A 366 0.10 SIDE CHAIN REMARK 500 18 ARG A 405 0.15 SIDE CHAIN REMARK 500 19 TYR A 366 0.12 SIDE CHAIN REMARK 500 20 TYR A 337 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 1 SER A 373 -10.40 REMARK 500 7 SER A 373 -10.36 REMARK 500 REMARK 500 REMARK: NULL DBREF 1NGR A 334 418 UNP P07174 TNR16_RAT 334 418 SEQRES 1 A 85 GLY ASN LEU TYR SER SER LEU PRO LEU THR LYS ARG GLU SEQRES 2 A 85 GLU VAL GLU LYS LEU LEU ASN GLY ASP THR TRP ARG HIS SEQRES 3 A 85 LEU ALA GLY GLU LEU GLY TYR GLN PRO GLU HIS ILE ASP SEQRES 4 A 85 SER PHE THR HIS GLU ALA CYS PRO VAL ARG ALA LEU LEU SEQRES 5 A 85 ALA SER TRP GLY ALA GLN ASP SER ALA THR LEU ASP ALA SEQRES 6 A 85 LEU LEU ALA ALA LEU ARG ARG ILE GLN ARG ALA ASP ILE SEQRES 7 A 85 VAL GLU SER LEU CYS SER GLU HELIX 1 A1 THR A 343 LEU A 351 5 9 HELIX 2 A2 THR A 356 GLU A 363 1 8 HELIX 3 A3 PRO A 368 THR A 375 1 8 HELIX 4 A4 PRO A 380 ALA A 390 1 11 HELIX 5 A5 LEU A 396 ARG A 405 1 10 HELIX 6 A6 ALA A 409 CYS A 416 1 8 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