HEADER PROTEIN BINDING 03-MAY-06 2GW6 TITLE NMR STRUCTURE OF THE HUMAN TRNA ENDONUCLEASE SEN15 SUBUNIT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA-SPLICING ENDONUCLEASE SUBUNIT SEN15; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRNA-INTRON ENDONUCLEASE SEN15, HSSEN15; COMPND 5 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: TSEN15, C1ORF19, SEN15; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVP13 KEYWDS SEN15_HUMAN, TRNA ENDONUCLEASE, STRUCTURAL GENOMICS, PSI, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS, KEYWDS 3 CESG, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.SONG,J.L.MARKLEY,CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 4 09-MAR-22 2GW6 1 REMARK SEQADV REVDAT 3 24-FEB-09 2GW6 1 VERSN REVDAT 2 30-SEP-08 2GW6 1 JRNL REVDAT 1 16-MAY-06 2GW6 0 JRNL AUTH J.SONG,J.L.MARKLEY JRNL TITL THREE-DIMENSIONAL STRUCTURE DETERMINED FOR A SUBUNIT OF JRNL TITL 2 HUMAN TRNA SPLICING ENDONUCLEASE (SEN15) REVEALS A NOVEL JRNL TITL 3 DIMERIC FOLD. JRNL REF J.MOL.BIOL. V. 366 155 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17166513 JRNL DOI 10.1016/J.JMB.2006.11.024 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 1.1, XPLOR-NIH 2.9.8 REMARK 3 AUTHORS : SCHWIETERS, C.D. ET AL. (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF REMARK 3 4516 NOE RESTRAINTS (1704 INTRA, 1038 SEQUENTIAL, 802 MEDIUM, REMARK 3 862 LONG RANGE INTERMOLECULAR AND 110 INTERMOLECULAR), 182 H BOND REMARK 3 RESTRAINTS, AND 326 PHI AND PSI REMARK 3 DIHEDRAL ANGLE CONSTRAINTS REMARK 4 REMARK 4 2GW6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037622. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM BIS-TRIS, 100MM NACL, 10 REMARK 210 MM DTT, 0.5 MM 13C, 15N-LABELED REMARK 210 SEN15_HUMAN, 90% H2O, 10% D2O; REMARK 210 20 MM BIS-TRIS,100MM NACL, 10 MM REMARK 210 DTT, 0.5 MM 13C, 15N-LABELED REMARK 210 SEN15_HUMAN, 0.5 MM UNLABELED REMARK 210 SEN15_HUMAN, 90% H2O, 10% D2O; REMARK 210 20 MM BIS-TRIS,100MM NACL, 10 MM REMARK 210 DTT, 0.5 MM 15N-LABELED SEN15_ REMARK 210 HUMAN, 17MG/ML PF1 PHAGE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H,15N-HSQC; 1H,13C-HSQC; REMARK 210 HNCACB; CBCACONH; CCONH; REMARK 210 HCCHTOCSY; HBACONH; 13C-EDITED REMARK 210 1H,1H-NOESY; 15C-EDITED 1H,1H- REMARK 210 NOESY; 13C,15N FILTERED, 13C REMARK 210 EDITED 1H,1H-NOESY; IPAP 1H,15N- REMARK 210 HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 97.027.12.56, SPARKY 3.72, CYANA REMARK 210 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,SIMULATED REMARK 210 ANNEALING,DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: 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: 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 ASP A 3 26.06 -149.06 REMARK 500 1 THR A 8 0.93 176.37 REMARK 500 1 ASP A 19 21.34 -74.82 REMARK 500 1 SER A 41 104.91 53.42 REMARK 500 1 GLU A 66 -159.16 -86.19 REMARK 500 1 GLN A 69 116.46 -160.39 REMARK 500 1 ALA B 304 25.45 -150.86 REMARK 500 1 TRP B 305 -40.07 -135.00 REMARK 500 1 ASP B 319 39.56 -76.04 REMARK 500 1 SER B 341 81.15 29.08 REMARK 500 1 GLN B 354 14.95 80.19 REMARK 500 1 GLU B 366 -160.85 -103.57 REMARK 500 1 PRO B 399 92.20 -66.69 REMARK 500 1 ASP B 400 65.74 36.82 REMARK 500 1 SER B 414 -18.10 174.59 REMARK 500 2 THR A 8 -64.80 -151.09 REMARK 500 2 ASP A 19 -18.75 39.12 REMARK 500 2 ILE A 20 -67.30 -156.21 REMARK 500 2 GLN A 69 116.64 -166.27 REMARK 500 2 ASP A 100 94.11 53.84 REMARK 500 2 PRO A 102 109.89 -55.80 REMARK 500 2 SER A 114 -38.71 176.23 REMARK 500 2 THR A 115 107.13 -50.46 REMARK 500 2 LEU B 318 172.78 -58.62 REMARK 500 2 ASP B 319 -5.88 -40.06 REMARK 500 2 ILE B 320 -62.04 -152.61 REMARK 500 2 GLU B 366 -161.43 -101.62 REMARK 500 2 LEU B 368 112.77 -163.01 REMARK 500 2 GLN B 369 114.34 -168.38 REMARK 500 2 THR B 377 9.94 -69.45 REMARK 500 2 PRO B 399 99.60 -62.94 REMARK 500 2 ASP B 400 47.06 33.25 REMARK 500 2 MET B 403 -165.84 -119.16 REMARK 500 3 ASP A 3 32.13 -53.33 REMARK 500 3 THR A 8 -5.30 175.69 REMARK 500 3 ASP A 19 35.17 -69.26 REMARK 500 3 ILE A 20 -60.03 -162.53 REMARK 500 3 SER A 41 72.72 39.28 REMARK 500 3 GLN A 69 117.90 -165.44 REMARK 500 3 ASP A 100 35.31 -49.73 REMARK 500 3 MET A 103 -167.99 -112.46 REMARK 500 3 SER A 114 16.35 161.64 REMARK 500 3 ASP B 319 39.47 -71.00 REMARK 500 3 ILE B 320 -54.75 -170.60 REMARK 500 3 SER B 341 73.32 37.36 REMARK 500 3 MET B 403 -153.16 -127.92 REMARK 500 3 SER B 414 0.64 164.48 REMARK 500 4 THR A 8 -46.47 99.19 REMARK 500 4 GLU A 66 -157.08 -86.16 REMARK 500 4 GLN A 69 118.77 -166.12 REMARK 500 REMARK 500 THIS ENTRY HAS 348 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 4 ARG B 393 0.08 SIDE CHAIN REMARK 500 7 ARG B 384 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.78856 RELATED DB: TARGETDB DBREF 2GW6 A 2 123 UNP Q8WW01 SEN15_HUMAN 36 157 DBREF 2GW6 B 302 423 UNP Q8WW01 SEN15_HUMAN 36 157 SEQADV 2GW6 SER A 1 UNP Q8WW01 CLONING ARTIFACT SEQADV 2GW6 SER B 301 UNP Q8WW01 CLONING ARTIFACT SEQRES 1 A 123 SER GLU ASP ALA TRP MET GLY THR HIS PRO LYS TYR LEU SEQRES 2 A 123 GLU MET MET GLU LEU ASP ILE GLY ASP ALA THR GLN VAL SEQRES 3 A 123 TYR VAL ALA PHE LEU VAL TYR LEU ASP LEU MET GLU SER SEQRES 4 A 123 LYS SER TRP HIS GLU VAL ASN CYS VAL GLY LEU PRO GLU SEQRES 5 A 123 LEU GLN LEU ILE CYS LEU VAL GLY THR GLU ILE GLU GLY SEQRES 6 A 123 GLU GLY LEU GLN THR VAL VAL PRO THR PRO ILE THR ALA SEQRES 7 A 123 SER LEU SER HIS ASN ARG ILE ARG GLU ILE LEU LYS ALA SEQRES 8 A 123 SER ARG LYS LEU GLN GLY ASP PRO ASP LEU PRO MET SER SEQRES 9 A 123 PHE THR LEU ALA ILE VAL GLU SER ASP SER THR ILE VAL SEQRES 10 A 123 TYR TYR LYS LEU THR ASP SEQRES 1 B 123 SER GLU ASP ALA TRP MET GLY THR HIS PRO LYS TYR LEU SEQRES 2 B 123 GLU MET MET GLU LEU ASP ILE GLY ASP ALA THR GLN VAL SEQRES 3 B 123 TYR VAL ALA PHE LEU VAL TYR LEU ASP LEU MET GLU SER SEQRES 4 B 123 LYS SER TRP HIS GLU VAL ASN CYS VAL GLY LEU PRO GLU SEQRES 5 B 123 LEU GLN LEU ILE CYS LEU VAL GLY THR GLU ILE GLU GLY SEQRES 6 B 123 GLU GLY LEU GLN THR VAL VAL PRO THR PRO ILE THR ALA SEQRES 7 B 123 SER LEU SER HIS ASN ARG ILE ARG GLU ILE LEU LYS ALA SEQRES 8 B 123 SER ARG LYS LEU GLN GLY ASP PRO ASP LEU PRO MET SER SEQRES 9 B 123 PHE THR LEU ALA ILE VAL GLU SER ASP SER THR ILE VAL SEQRES 10 B 123 TYR TYR LYS LEU THR ASP HELIX 1 1 HIS A 9 GLU A 17 1 9 HELIX 2 2 ASP A 22 SER A 39 1 18 HELIX 3 3 HIS A 82 GLN A 96 1 15 HELIX 4 4 HIS B 309 GLU B 317 1 9 HELIX 5 5 ASP B 322 LYS B 340 1 19 HELIX 6 6 HIS B 382 GLY B 397 1 16 SHEET 1 A 6 GLU A 44 LEU A 50 0 SHEET 2 A 6 LEU A 55 THR A 61 -1 O CYS A 57 N VAL A 48 SHEET 3 A 6 THR A 70 PRO A 75 -1 O VAL A 71 N LEU A 58 SHEET 4 A 6 SER A 104 VAL A 110 1 O ALA A 108 N THR A 74 SHEET 5 A 6 ILE A 116 THR A 122 -1 O VAL A 117 N ILE A 109 SHEET 6 A 6 LEU B 380 SER B 381 1 O LEU B 380 N THR A 122 SHEET 1 B 6 SER A 79 SER A 81 0 SHEET 2 B 6 ILE B 416 THR B 422 1 O LYS B 420 N LEU A 80 SHEET 3 B 6 SER B 404 VAL B 410 -1 N LEU B 407 O TYR B 419 SHEET 4 B 6 LEU B 368 PRO B 375 1 N THR B 370 O THR B 406 SHEET 5 B 6 LEU B 355 THR B 361 -1 N LEU B 358 O VAL B 371 SHEET 6 B 6 GLU B 344 LEU B 350 -1 N VAL B 348 O CYS B 357 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