PDB Short entry for 2N97 HEADER SIGNALING PROTEIN 07-NOV-15 2N97 TITLE DD HOMODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 334-427; COMPND 5 SYNONYM: GP80-LNGFR, LOW AFFINITY NEUROTROPHIN RECEPTOR P75NTR, LOW- COMPND 6 AFFINITY NERVE GROWTH FACTOR RECEPTOR, NGF RECEPTOR, P75 ICD; 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: NGFR, TNFRSF16; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET32A-DERIVED KEYWDS DEATH DOMAIN, P75NTR, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.LIN,C.F.IBANEZ REVDAT 3 14-JUN-23 2N97 1 REMARK REVDAT 2 27-APR-16 2N97 1 ATOM DBREF REMARK SEQRES REVDAT 1 23-DEC-15 2N97 0 JRNL AUTH Z.LIN,J.Y.TANN,E.T.GOH,C.KELLY,K.B.LIM,J.F.GAO,C.F.IBANEZ JRNL TITL STRUCTURAL BASIS OF DEATH DOMAIN SIGNALING IN THE P75 JRNL TITL 2 NEUROTROPHIN RECEPTOR JRNL REF ELIFE V. 4 11692 2015 JRNL REFN ESSN 2050-084X JRNL PMID 26646181 JRNL DOI 10.7554/ELIFE.11692 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, AMBER REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), CASE, DARDEN, CHEATHAM, III, SIMMERLING, REMARK 3 WANG, DUKE, LUO, ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N97 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000104580. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 P75NTR DD-1, 10 MM [U-98% 2H] REMARK 210 DTT-2, 1 MM P75NTR DD-3, 50 MM REMARK 210 SODIUM PHOSPHATE-4, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HCCH-TOCSY; 3D 13C,15N- REMARK 210 FILTERED NOESY; 3D 13C, 15N- REMARK 210 EDITED NOESY; 3D HN(CO)CA; 4D REMARK 210 13C, 15N-EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, CYANA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: DIMERIC 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 LYS A 330 REMARK 465 GLY A 331 REMARK 465 ASP A 332 REMARK 465 GLY A 333 REMARK 465 LYS B 330 REMARK 465 GLY B 331 REMARK 465 ASP B 332 REMARK 465 GLY B 333 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 3 ARG B 384 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG B 407 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG B 410 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG B 410 NE - CZ - NH1 ANGL. DEV. = 3.2 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 354 -62.24 -99.46 REMARK 500 1 CYS A 381 71.26 -112.84 REMARK 500 1 ALA A 396 23.75 -69.64 REMARK 500 1 THR A 424 32.65 -141.35 REMARK 500 1 ALA B 355 92.12 -163.71 REMARK 500 1 CYS B 381 67.17 -115.82 REMARK 500 1 ALA B 396 26.33 -68.49 REMARK 500 2 ALA A 355 93.63 -38.30 REMARK 500 2 CYS A 381 70.66 -113.37 REMARK 500 2 ALA A 396 25.44 -67.57 REMARK 500 2 ALA B 355 60.68 -164.65 REMARK 500 2 CYS B 381 68.04 -118.03 REMARK 500 2 ALA B 396 25.41 -70.46 REMARK 500 2 THR B 422 70.37 24.81 REMARK 500 3 ALA A 355 109.91 -167.51 REMARK 500 3 THR A 377 2.93 -69.15 REMARK 500 3 CYS A 381 67.08 -117.68 REMARK 500 3 ALA A 396 22.49 -69.88 REMARK 500 3 THR A 424 -80.34 -134.92 REMARK 500 3 CYS B 381 72.64 -112.34 REMARK 500 3 ALA B 396 34.97 -69.27 REMARK 500 3 SER B 421 51.04 -116.87 REMARK 500 3 THR B 422 34.95 -70.75 REMARK 500 3 SER B 425 59.85 32.66 REMARK 500 4 ALA A 355 -55.60 -153.96 REMARK 500 4 CYS A 381 71.06 -113.92 REMARK 500 4 ALA A 396 24.28 -67.93 REMARK 500 4 THR A 424 47.14 -144.28 REMARK 500 4 SER A 425 158.07 74.83 REMARK 500 4 SER B 354 -60.05 -108.02 REMARK 500 4 CYS B 381 70.95 -116.12 REMARK 500 4 ALA B 396 25.87 -69.56 REMARK 500 5 ALA A 355 82.79 -163.11 REMARK 500 5 CYS A 381 66.82 -117.66 REMARK 500 5 ALA A 396 28.07 -67.21 REMARK 500 5 ALA B 355 117.27 -164.46 REMARK 500 5 CYS B 381 67.86 -112.08 REMARK 500 5 ALA B 396 25.16 -68.10 REMARK 500 6 ALA A 355 104.57 -163.36 REMARK 500 6 CYS A 381 67.58 -110.54 REMARK 500 6 ALA A 396 22.52 -70.79 REMARK 500 6 SER A 421 24.89 -75.03 REMARK 500 6 THR A 422 12.55 -146.94 REMARK 500 6 THR A 424 -72.31 -151.47 REMARK 500 6 SER B 354 21.90 -62.74 REMARK 500 6 ALA B 355 11.28 -142.27 REMARK 500 6 CYS B 381 67.82 -110.86 REMARK 500 6 ALA B 396 25.38 -67.85 REMARK 500 6 THR B 422 59.63 35.95 REMARK 500 6 PRO B 426 98.88 -69.43 REMARK 500 REMARK 500 THIS ENTRY HAS 84 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25883 RELATED DB: BMRB REMARK 900 RELATED ID: 2N7Z RELATED DB: PDB REMARK 900 RELATED ID: 2N80 RELATED DB: PDB REMARK 900 RELATED ID: 2N83 RELATED DB: PDB DBREF 2N97 A 330 427 UNP P08138 TNR16_HUMAN 330 427 DBREF 2N97 B 330 427 UNP P08138 TNR16_HUMAN 330 427 SEQRES 1 A 98 LYS GLY ASP GLY GLY LEU TYR SER SER LEU PRO PRO ALA SEQRES 2 A 98 LYS ARG GLU GLU VAL GLU LYS LEU LEU ASN GLY SER ALA SEQRES 3 A 98 GLY ASP THR TRP ARG HIS LEU ALA GLY GLU LEU GLY TYR SEQRES 4 A 98 GLN PRO GLU HIS ILE ASP SER PHE THR HIS GLU ALA CYS SEQRES 5 A 98 PRO VAL ARG ALA LEU LEU ALA SER TRP ALA THR GLN ASP SEQRES 6 A 98 SER ALA THR LEU ASP ALA LEU LEU ALA ALA LEU ARG ARG SEQRES 7 A 98 ILE GLN ARG ALA ASP LEU VAL GLU SER LEU CYS SER GLU SEQRES 8 A 98 SER THR ALA THR SER PRO VAL SEQRES 1 B 98 LYS GLY ASP GLY GLY LEU TYR SER SER LEU PRO PRO ALA SEQRES 2 B 98 LYS ARG GLU GLU VAL GLU LYS LEU LEU ASN GLY SER ALA SEQRES 3 B 98 GLY ASP THR TRP ARG HIS LEU ALA GLY GLU LEU GLY TYR SEQRES 4 B 98 GLN PRO GLU HIS ILE ASP SER PHE THR HIS GLU ALA CYS SEQRES 5 B 98 PRO VAL ARG ALA LEU LEU ALA SER TRP ALA THR GLN ASP SEQRES 6 B 98 SER ALA THR LEU ASP ALA LEU LEU ALA ALA LEU ARG ARG SEQRES 7 B 98 ILE GLN ARG ALA ASP LEU VAL GLU SER LEU CYS SER GLU SEQRES 8 B 98 SER THR ALA THR SER PRO VAL HELIX 1 1 LEU A 335 LEU A 339 5 5 HELIX 2 2 PRO A 340 SER A 354 1 15 HELIX 3 3 ASP A 357 LEU A 366 1 10 HELIX 4 4 GLN A 369 THR A 377 1 9 HELIX 5 5 CYS A 381 THR A 392 1 12 HELIX 6 6 THR A 397 ILE A 408 1 12 HELIX 7 7 ARG A 410 GLU A 420 1 11 HELIX 8 8 LEU B 335 LEU B 339 5 5 HELIX 9 9 PRO B 340 SER B 354 1 15 HELIX 10 10 ASP B 357 GLY B 367 1 11 HELIX 11 11 GLN B 369 THR B 377 1 9 HELIX 12 12 CYS B 381 ALA B 391 1 11 HELIX 13 13 THR B 397 ILE B 408 1 12 HELIX 14 14 ARG B 410 GLU B 420 1 11 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