HEADER RNA BINDING PROTEIN/RNA 29-OCT-10 2L5D TITLE SOLUTION STRUCTURES OF HUMAN PIWI-LIKE 1 PAZ DOMAIN WITH SSRNA (5'- TITLE 2 PUGACA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PAZ DOMAIN, UNP RESIDUES 266-399; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*UP*GP*AP*CP*A)-3'; COMPND 8 CHAIN: B; COMPND 9 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: PIWIL1, HIWI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS PIWI, PAZ, PIRNA, SSRNA, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.ZENG,Q.ZHANG,K.YAN,M.ZHOU REVDAT 3 01-MAY-24 2L5D 1 REMARK REVDAT 2 25-MAY-11 2L5D 1 JRNL REVDAT 1 20-APR-11 2L5D 0 JRNL AUTH L.ZENG,Q.ZHANG,K.YAN,M.M.ZHOU JRNL TITL STRUCTURAL INSIGHTS INTO PIRNA RECOGNITION BY THE HUMAN JRNL TITL 2 PIWI-LIKE 1 PAZ DOMAIN. JRNL REF PROTEINS V. 79 2004 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 21465557 JRNL DOI 10.1002/PROT.23003 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000101977. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 100 MM SODIUM PHOSPHATE-1, 150 REMARK 210 MM SODIUM CHLORIDE-2, 5 MM [U- REMARK 210 100% 2H] DTT-3, 100% D2O; 100 MM REMARK 210 SODIUM PHOSPHATE-4, 150 MM REMARK 210 SODIUM CHLORIDE-5, 5 MM [U-100% REMARK 210 2H] DTT-6, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HN(COCA)CB; 3D 1H REMARK 210 -15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 13C-EDITED-13C/15N-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, NMRVIEW 5.04, CNS REMARK 210 1.2 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 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 H GLY A 391 H LEU A 392 1.17 REMARK 500 HD2 HIS A 293 H LYS A 294 1.31 REMARK 500 O SER A 300 H ILE A 304 1.54 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 18 TYR A 350 CB - CG - CD1 ANGL. DEV. = 4.9 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 270 179.50 51.91 REMARK 500 1 HIS A 271 116.03 -166.04 REMARK 500 1 LYS A 272 83.39 -65.05 REMARK 500 1 VAL A 273 86.65 26.63 REMARK 500 1 GLU A 277 126.81 167.63 REMARK 500 1 GLN A 289 -99.46 -117.17 REMARK 500 1 THR A 290 162.00 -41.23 REMARK 500 1 GLU A 291 -156.11 -62.78 REMARK 500 1 PHE A 295 -78.76 -41.89 REMARK 500 1 ASN A 314 53.83 23.28 REMARK 500 1 TRP A 324 43.85 -79.33 REMARK 500 1 ASP A 325 -54.88 -136.63 REMARK 500 1 PRO A 328 10.83 -66.84 REMARK 500 1 SER A 330 133.85 -33.35 REMARK 500 1 GLU A 344 -70.96 -69.27 REMARK 500 1 ASN A 351 72.16 52.18 REMARK 500 1 GLU A 353 100.81 24.45 REMARK 500 1 THR A 355 -62.47 76.83 REMARK 500 1 LEU A 357 23.55 -72.34 REMARK 500 1 PRO A 360 -153.83 -81.92 REMARK 500 1 LYS A 367 48.62 29.97 REMARK 500 1 ARG A 368 161.93 -44.65 REMARK 500 1 ARG A 370 11.82 49.45 REMARK 500 1 PRO A 372 -74.38 -86.08 REMARK 500 1 THR A 375 113.02 54.80 REMARK 500 1 ALA A 380 147.49 -175.75 REMARK 500 1 THR A 390 -127.57 -105.53 REMARK 500 1 MET A 396 114.84 -17.17 REMARK 500 1 ARG A 397 -44.89 -157.36 REMARK 500 1 ASN A 398 53.23 76.18 REMARK 500 2 VAL A 273 84.38 25.99 REMARK 500 2 ARG A 275 -72.07 -92.61 REMARK 500 2 SER A 276 -153.34 -110.61 REMARK 500 2 GLU A 277 123.92 75.74 REMARK 500 2 GLN A 289 -102.13 -60.40 REMARK 500 2 THR A 290 160.98 -40.94 REMARK 500 2 GLU A 291 -156.26 -62.70 REMARK 500 2 PHE A 295 -78.04 -38.05 REMARK 500 2 ASN A 314 70.41 23.39 REMARK 500 2 ASP A 323 87.20 -67.54 REMARK 500 2 TRP A 324 40.76 -79.03 REMARK 500 2 ASP A 325 -55.18 -132.83 REMARK 500 2 PRO A 328 12.50 -67.06 REMARK 500 2 SER A 330 147.43 -33.35 REMARK 500 2 GLN A 352 78.79 -106.96 REMARK 500 2 THR A 355 -64.83 75.76 REMARK 500 2 LEU A 357 6.74 45.63 REMARK 500 2 PRO A 360 -154.31 -84.13 REMARK 500 2 ARG A 369 -169.06 -103.70 REMARK 500 2 PRO A 372 -139.80 -95.99 REMARK 500 REMARK 500 THIS ENTRY HAS 576 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2L5D A 266 399 UNP Q96J94 PIWL1_HUMAN 266 399 DBREF 2L5D B 501 505 PDB 2L5D 2L5D 501 505 SEQRES 1 A 134 CYS THR ASP VAL SER HIS LYS VAL LEU ARG SER GLU THR SEQRES 2 A 134 VAL LEU ASP PHE MET PHE ASN PHE TYR HIS GLN THR GLU SEQRES 3 A 134 GLU HIS LYS PHE GLN GLU GLN VAL SER LYS GLU LEU ILE SEQRES 4 A 134 GLY LEU VAL VAL LEU THR LYS TYR ASN ASN LYS THR TYR SEQRES 5 A 134 ARG VAL ASP ASP ILE ASP TRP ASP GLN ASN PRO LYS SER SEQRES 6 A 134 THR PHE LYS LYS ALA ASP GLY SER GLU VAL SER PHE LEU SEQRES 7 A 134 GLU TYR TYR ARG LYS GLN TYR ASN GLN GLU ILE THR ASP SEQRES 8 A 134 LEU LYS GLN PRO VAL LEU VAL SER GLN PRO LYS ARG ARG SEQRES 9 A 134 ARG GLY PRO GLY GLY THR LEU PRO GLY PRO ALA MET LEU SEQRES 10 A 134 ILE PRO GLU LEU CYS TYR LEU THR GLY LEU THR ASP LYS SEQRES 11 A 134 MET ARG ASN ASP SEQRES 1 B 5 U G A C A HELIX 1 1 THR A 278 PHE A 286 1 9 HELIX 2 2 TYR A 287 GLN A 289 5 3 HELIX 3 3 GLU A 292 ILE A 304 1 13 HELIX 4 4 PHE A 342 TYR A 350 1 9 SHEET 1 A 5 ALA A 380 LEU A 382 0 SHEET 2 A 5 VAL A 361 SER A 364 -1 N SER A 364 O ALA A 380 SHEET 3 A 5 LYS A 315 ASP A 323 -1 N ASP A 323 O VAL A 361 SHEET 4 A 5 LEU A 306 THR A 310 -1 N THR A 310 O LYS A 315 SHEET 5 A 5 CYS A 387 LEU A 389 -1 O TYR A 388 N LEU A 309 SHEET 1 B 2 THR A 331 PHE A 332 0 SHEET 2 B 2 VAL A 340 SER A 341 -1 O VAL A 340 N PHE A 332 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