PDB Short entry for 2N80 HEADER SIGNALING PROTEIN 30-SEP-15 2N80 TITLE P75NTR DD:RHOGDI COMPND MOL_ID: 1; COMPND 2 MOLECULE: TUMOR NECROSIS FACTOR RECEPTOR SUPERFAMILY MEMBER 16; COMPND 3 CHAIN: A; 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; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RHO GDP-DISSOCIATION INHIBITOR 1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 31-204; COMPND 12 SYNONYM: RHO GDI 1, RHO-GDI ALPHA; COMPND 13 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; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: ARHGDIA, GDIA1; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR KEYWDS RHOGDI, P75NTR, DEATH DOMAIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Z.LIN,C.F.IBANEZ REVDAT 1 23-DEC-15 2N80 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 : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N80 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-OCT-15. REMARK 100 THE RCSB ID CODE IS RCSB104537. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 301 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 10 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 P75NTR DD-1, 1 MM [U-98% 2H] DTT- REMARK 210 2, 10 MM [U-98% 2H] HEPES-3, 1 MM REMARK 210 EDTA-4, 1 MM SODIUM AZIDE-5, 2 MM REMARK 210 RHOGDI-6, 95% H2O/5% D2O; 0.5 MM REMARK 210 [U-99% 13C; U-99% 15N] RHOGDI-7, REMARK 210 2 MM P75NTR DD-8, 1 MM [U-98% 2H] REMARK 210 DTT-9, 10 MM [U-98% 2H] HEPES-10, REMARK 210 1 MM EDTA-11, 1 MM SODIUM AZIDE- REMARK 210 12, 95% H2O/5% 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 HNCA; 3D HN(CO)CA; REMARK 210 3D HCCH-TOCSY; 3D 13C,15N- REMARK 210 FILTERED NOESY; 4D 13C, 15N- REMARK 210 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 : NMRPIPE, 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 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 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 B 120 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 410 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG B 172 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ALA A 396 40.75 -68.59 REMARK 500 1 SER A 421 28.53 -74.44 REMARK 500 1 ALA A 423 92.53 -66.36 REMARK 500 1 SER A 425 68.37 -162.43 REMARK 500 1 LYS B 33 47.60 -147.63 REMARK 500 1 SER B 34 -38.50 -138.34 REMARK 500 1 ARG B 58 45.47 -148.37 REMARK 500 1 VAL B 59 10.11 -63.24 REMARK 500 1 VAL B 61 17.10 53.24 REMARK 500 1 VAL B 72 109.60 -59.95 REMARK 500 1 ASP B 93 67.86 -69.42 REMARK 500 1 ARG B 120 -65.99 -145.06 REMARK 500 1 PRO B 151 49.14 -74.98 REMARK 500 1 GLU B 154 -168.88 -100.08 REMARK 500 1 TRP B 202 13.69 -158.88 REMARK 500 1 LYS B 203 -32.70 -160.92 REMARK 500 2 ALA A 396 38.31 -68.91 REMARK 500 2 ILE B 35 49.52 -72.98 REMARK 500 2 CYS B 79 101.15 -160.15 REMARK 500 2 LEU B 90 29.64 -140.59 REMARK 500 2 ASP B 93 96.81 -59.18 REMARK 500 2 ARG B 120 41.24 -175.43 REMARK 500 2 TRP B 202 13.02 -152.03 REMARK 500 2 LYS B 203 54.63 -166.61 REMARK 500 3 ALA A 355 159.46 169.41 REMARK 500 3 ALA A 396 53.12 -68.29 REMARK 500 3 SER A 421 49.65 -77.66 REMARK 500 3 ILE B 38 -36.66 -149.76 REMARK 500 3 GLU B 40 1.84 -66.24 REMARK 500 3 ALA B 60 56.62 -90.67 REMARK 500 3 SER B 62 50.95 -116.98 REMARK 500 3 LEU B 90 36.56 -142.31 REMARK 500 3 ASP B 93 85.23 -60.93 REMARK 500 3 ARG B 120 -69.96 -147.60 REMARK 500 3 GLU B 154 -167.77 -101.95 REMARK 500 3 TRP B 202 11.81 -160.26 REMARK 500 3 LYS B 203 -40.95 -169.41 REMARK 500 4 SER A 354 -178.06 -62.57 REMARK 500 4 ALA A 396 37.27 -68.51 REMARK 500 4 SER A 421 32.12 -77.24 REMARK 500 4 THR A 422 59.88 -69.94 REMARK 500 4 GLN B 32 -21.21 -148.89 REMARK 500 4 GLU B 40 1.75 -61.71 REMARK 500 4 ASP B 44 24.93 -144.43 REMARK 500 4 ARG B 58 44.76 -83.92 REMARK 500 4 CYS B 79 97.88 -164.82 REMARK 500 4 ARG B 120 40.36 -179.68 REMARK 500 4 LYS B 203 -25.96 -163.41 REMARK 500 5 SER A 354 170.35 -58.96 REMARK 500 5 ALA A 396 33.27 -67.74 REMARK 500 REMARK 500 THIS ENTRY HAS 120 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 3 TYR B 175 0.08 SIDE CHAIN REMARK 500 4 TYR B 175 0.09 SIDE CHAIN REMARK 500 5 ARG A 384 0.09 SIDE CHAIN REMARK 500 6 TYR B 175 0.07 SIDE CHAIN REMARK 500 8 TYR B 175 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25829 RELATED DB: BMRB REMARK 900 RELATED ID: 2N7Z RELATED DB: PDB REMARK 900 RELATED ID: 2N83 RELATED DB: PDB REMARK 900 RELATED ID: 2N97 RELATED DB: PDB DBREF 2N80 A 334 427 UNP P08138 TNR16_HUMAN 334 427 DBREF 2N80 B 31 204 UNP P52565 GDIR1_HUMAN 31 204 SEQRES 1 A 94 GLY LEU TYR SER SER LEU PRO PRO ALA LYS ARG GLU GLU SEQRES 2 A 94 VAL GLU LYS LEU LEU ASN GLY SER ALA GLY ASP THR TRP SEQRES 3 A 94 ARG HIS LEU ALA GLY GLU LEU GLY TYR GLN PRO GLU HIS SEQRES 4 A 94 ILE ASP SER PHE THR HIS GLU ALA CYS PRO VAL ARG ALA SEQRES 5 A 94 LEU LEU ALA SER TRP ALA THR GLN ASP SER ALA THR LEU SEQRES 6 A 94 ASP ALA LEU LEU ALA ALA LEU ARG ARG ILE GLN ARG ALA SEQRES 7 A 94 ASP LEU VAL GLU SER LEU CYS SER GLU SER THR ALA THR SEQRES 8 A 94 SER PRO VAL SEQRES 1 B 174 ALA GLN LYS SER ILE GLN GLU ILE GLN GLU LEU ASP LYS SEQRES 2 B 174 ASP ASP GLU SER LEU ARG LYS TYR LYS GLU ALA LEU LEU SEQRES 3 B 174 GLY ARG VAL ALA VAL SER ALA ASP PRO ASN VAL PRO ASN SEQRES 4 B 174 VAL VAL VAL THR GLY LEU THR LEU VAL CYS SER SER ALA SEQRES 5 B 174 PRO GLY PRO LEU GLU LEU ASP LEU THR GLY ASP LEU GLU SEQRES 6 B 174 SER PHE LYS LYS GLN SER PHE VAL LEU LYS GLU GLY VAL SEQRES 7 B 174 GLU TYR ARG ILE LYS ILE SER PHE ARG VAL ASN ARG GLU SEQRES 8 B 174 ILE VAL SER GLY MET LYS TYR ILE GLN HIS THR TYR ARG SEQRES 9 B 174 LYS GLY VAL LYS ILE ASP LYS THR ASP TYR MET VAL GLY SEQRES 10 B 174 SER TYR GLY PRO ARG ALA GLU GLU TYR GLU PHE LEU THR SEQRES 11 B 174 PRO VAL GLU GLU ALA PRO LYS GLY MET LEU ALA ARG GLY SEQRES 12 B 174 SER TYR SER ILE LYS SER ARG PHE THR ASP ASP ASP LYS SEQRES 13 B 174 THR ASP HIS LEU SER TRP GLU TRP ASN LEU THR ILE LYS SEQRES 14 B 174 LYS ASP TRP LYS ASP HELIX 1 1 LEU A 335 LEU A 339 5 5 HELIX 2 2 PRO A 340 ASN A 352 1 13 HELIX 3 3 ASP A 357 GLY A 367 1 11 HELIX 4 4 GLN A 369 HIS A 378 1 10 HELIX 5 5 CYS A 381 ALA A 391 1 11 HELIX 6 6 THR A 397 ILE A 408 1 12 HELIX 7 7 ARG A 410 CYS A 418 1 9 HELIX 8 8 SER B 34 GLN B 39 5 6 HELIX 9 9 GLU B 40 SER B 47 1 8 HELIX 10 10 LEU B 48 ALA B 54 1 7 HELIX 11 11 LEU B 55 VAL B 59 5 5 HELIX 12 12 GLY B 168 ARG B 172 5 5 SHEET 1 A 4 LEU B 86 ASP B 89 0 SHEET 2 A 4 VAL B 70 VAL B 78 -1 N LEU B 75 O LEU B 88 SHEET 3 A 4 GLU B 109 VAL B 118 -1 O LYS B 113 N THR B 76 SHEET 4 A 4 GLU B 155 LEU B 159 -1 O TYR B 156 N PHE B 116 SHEET 1 B 4 LEU B 86 ASP B 89 0 SHEET 2 B 4 VAL B 70 VAL B 78 -1 N LEU B 75 O LEU B 88 SHEET 3 B 4 GLU B 109 VAL B 118 -1 O LYS B 113 N THR B 76 SHEET 4 B 4 GLU B 163 GLU B 164 -1 O GLU B 163 N TYR B 110 SHEET 1 C 5 SER B 101 LYS B 105 0 SHEET 2 C 5 LEU B 190 LYS B 199 1 O LYS B 199 N LEU B 104 SHEET 3 C 5 SER B 174 THR B 182 -1 N ILE B 177 O TRP B 194 SHEET 4 C 5 VAL B 123 ARG B 134 -1 N ILE B 129 O ARG B 180 SHEET 5 C 5 VAL B 137 TYR B 149 -1 O TYR B 144 N TYR B 128 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