HEADER RNA/PROTEIN 27-MAY-10 2XFM TITLE COMPLEX STRUCTURE OF THE MIWI PAZ DOMAIN BOUND TO METHYLATED SINGLE TITLE 2 STRANDED RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PIWI-LIKE PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PAZ-DOMAIN, RESIDUES 276-425; COMPND 5 SYNONYM: MIWI; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*AP*CP*CP*GP*AP*CP*UP*(OMU)P)-3'; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: PIRNA; COMPND 11 OTHER_DETAILS: RNA WITH 3'-TERMINAL O2'-METHYL URIDINE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: BASED ON BIOLOGICAL SEQUENCE KEYWDS RNA-PROTEIN COMPLEX, DIFFERENTIATION, RNA INTERFERENCE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR B.SIMON,J.P.KIRKPATRICK,S.ECKHARDT,P.SEHR,M.A.ANDRADE-NAVARRO, AUTHOR 2 R.S.PILLAI,T.CARLOMAGNO REVDAT 2 26-OCT-11 2XFM 1 JRNL REMARK DBREF VERSN REVDAT 1 26-JAN-11 2XFM 0 JRNL AUTH B.SIMON,J.P.KIRKPATRICK,S.ECKHARDT,M.REUTER,E.A.ROCHA, JRNL AUTH 2 M.A.ANDRADE-NAVARRO,P.SEHR,R.S.PILLAI,T.CARLOMAGNO JRNL TITL RECOGNITION OF 2'-O-METHYLATED 3'-END OF PIRNA BY THE PAZ JRNL TITL 2 DOMAIN OF A PIWI PROTEIN. JRNL REF STRUCTURE V. 19 172 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 21237665 JRNL DOI 10.1016/J.STR.2010.11.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2XFM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-10. REMARK 100 THE PDBE ID CODE IS EBI-44082. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300.0 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 150MM REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TRIPLE RESONANCE; NOESY; EDITED REMARK 210 -FILTERED 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 REMARK 210 METHOD USED : ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NONE 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 396 REMARK 465 MET A 397 REMARK 465 ARG A 398 REMARK 465 ASN A 399 REMARK 465 ASP A 400 REMARK 465 PHE A 401 REMARK 465 ASN A 402 REMARK 465 VAL A 403 REMARK 465 MET A 404 REMARK 465 LYS A 405 REMARK 465 ASP A 406 REMARK 465 LEU A 407 REMARK 465 ALA A 408 REMARK 465 VAL A 409 REMARK 465 HIS A 410 REMARK 465 THR A 411 REMARK 465 ARG A 412 REMARK 465 LEU A 413 REMARK 465 THR A 414 REMARK 465 PRO A 415 REMARK 465 GLU A 416 REMARK 465 GLN A 417 REMARK 465 ARG A 418 REMARK 465 GLN A 419 REMARK 465 ARG A 420 REMARK 465 GLU A 421 REMARK 465 VAL A 422 REMARK 465 GLY A 423 REMARK 465 ARG A 424 REMARK 465 LEU A 425 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 HG3 GLU A 292 HB2 LYS A 295 1.42 REMARK 500 HB3 TYR A 313 HE2 TYR A 347 1.43 REMARK 500 HG12 VAL A 309 HB3 CYS A 388 1.43 REMARK 500 HG13 VAL A 280 HD12 LEU A 363 1.48 REMARK 500 HD12 LEU A 304 HD23 LEU A 307 1.50 REMARK 500 HG23 THR A 311 HG LEU A 383 1.52 REMARK 500 HD21 LEU A 390 HG23 THR A 394 1.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 2 TYR A 389 CE1 TYR A 389 CZ 0.101 REMARK 500 2 TYR A 389 CZ TYR A 389 CE2 -0.108 REMARK 500 5 TYR A 389 CZ TYR A 389 CE2 -0.087 REMARK 500 6 TYR A 389 CE1 TYR A 389 CZ 0.078 REMARK 500 6 TYR A 389 CZ TYR A 389 CE2 -0.084 REMARK 500 8 TYR A 347 CE1 TYR A 347 CZ -0.080 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 1 C B 3 C1' - O4' - C4' ANGL. DEV. = -5.6 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 277 139.90 67.67 REMARK 500 1 ASP A 337 75.59 51.57 REMARK 500 1 ASN A 352 17.78 -69.62 REMARK 500 1 THR A 356 36.04 -152.03 REMARK 500 1 LEU A 358 90.70 48.77 REMARK 500 1 ARG A 369 -178.24 -69.08 REMARK 500 1 ARG A 370 90.83 -66.09 REMARK 500 1 ARG A 371 -46.58 -149.48 REMARK 500 2 ILE A 305 97.03 -67.87 REMARK 500 2 ASN A 315 27.88 44.16 REMARK 500 2 ALA A 336 -100.11 65.54 REMARK 500 2 ASP A 337 76.07 -162.01 REMARK 500 2 THR A 356 44.48 -108.40 REMARK 500 2 LYS A 359 41.21 85.08 REMARK 500 2 LYS A 368 77.17 76.71 REMARK 500 3 ASN A 314 13.87 -152.45 REMARK 500 3 ASN A 315 36.62 39.11 REMARK 500 3 ASP A 326 35.60 70.49 REMARK 500 3 LYS A 368 46.08 -89.03 REMARK 500 3 LEU A 377 91.80 60.53 REMARK 500 4 THR A 311 -92.74 -69.44 REMARK 500 4 LYS A 312 -80.74 178.30 REMARK 500 4 ASN A 315 21.03 49.29 REMARK 500 4 PRO A 329 -9.71 -57.14 REMARK 500 4 ALA A 336 10.68 -158.37 REMARK 500 4 ASP A 337 79.49 40.68 REMARK 500 4 ASP A 357 -97.42 -122.71 REMARK 500 4 LEU A 358 87.73 66.14 REMARK 500 4 GLN A 366 91.16 58.30 REMARK 500 4 PRO A 367 34.99 -73.69 REMARK 500 4 ARG A 369 12.04 58.95 REMARK 500 4 LEU A 377 144.95 -171.56 REMARK 500 5 ASP A 337 79.15 45.39 REMARK 500 5 ARG A 371 -52.44 -124.09 REMARK 500 5 LEU A 377 76.25 61.06 REMARK 500 6 SER A 277 117.51 68.94 REMARK 500 6 THR A 311 -97.87 -76.72 REMARK 500 6 LYS A 312 -58.80 -178.70 REMARK 500 6 ASN A 315 37.13 34.01 REMARK 500 6 ALA A 336 -105.42 -158.94 REMARK 500 6 ASP A 337 -0.35 -142.02 REMARK 500 6 ASP A 357 44.90 -84.00 REMARK 500 6 ARG A 369 -56.02 68.49 REMARK 500 6 ARG A 371 89.81 65.76 REMARK 500 6 LEU A 393 28.87 -75.20 REMARK 500 7 SER A 277 146.13 72.67 REMARK 500 7 TYR A 313 -19.67 75.20 REMARK 500 7 PRO A 329 -9.65 -59.53 REMARK 500 7 ALA A 336 -27.19 -174.02 REMARK 500 7 ASP A 337 72.17 66.92 REMARK 500 REMARK 500 THIS ENTRY HAS 77 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED. DBREF 2XFM A 276 425 UNP Q9JMB7 PIWL1_MOUSE 276 425 DBREF 2XFM B 1 8 PDB 2XFM 2XFM 1 8 SEQRES 1 A 150 ARG SER GLU THR VAL LEU ASP PHE MET PHE ASN LEU TYR SEQRES 2 A 150 GLN GLN THR GLU GLU HIS LYS PHE GLN GLU GLN VAL SER SEQRES 3 A 150 LYS GLU LEU ILE GLY LEU ILE VAL LEU THR LYS TYR ASN SEQRES 4 A 150 ASN LYS THR TYR ARG VAL ASP ASP ILE ASP TRP ASP GLN SEQRES 5 A 150 ASN PRO LYS SER THR PHE LYS LYS ALA ASP GLY SER GLU SEQRES 6 A 150 VAL SER PHE LEU GLU TYR TYR ARG LYS GLN TYR ASN GLN SEQRES 7 A 150 GLU ILE THR ASP LEU LYS GLN PRO VAL LEU VAL SER GLN SEQRES 8 A 150 PRO LYS ARG ARG ARG GLY PRO GLY GLY THR LEU PRO GLY SEQRES 9 A 150 PRO ALA MET LEU ILE PRO GLU LEU CYS TYR LEU THR GLY SEQRES 10 A 150 LEU THR ASP LYS MET ARG ASN ASP PHE ASN VAL MET LYS SEQRES 11 A 150 ASP LEU ALA VAL HIS THR ARG LEU THR PRO GLU GLN ARG SEQRES 12 A 150 GLN ARG GLU VAL GLY ARG LEU SEQRES 1 B 8 A C C G A C U OMU MODRES 2XFM OMU B 8 U O2'-METHYLURIDINE 5'-MONOPHOSPHATE HET OMU B 8 34 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE FORMUL 2 OMU C10 H15 N2 O9 P HELIX 1 1 THR A 279 THR A 291 1 13 HELIX 2 2 GLU A 292 ILE A 305 1 14 HELIX 3 3 SER A 342 LYS A 349 1 8 HELIX 4 4 ILE A 384 GLU A 386 5 3 SHEET 1 AA 3 LYS A 316 ARG A 319 0 SHEET 2 AA 3 ILE A 308 THR A 311 -1 O VAL A 309 N TYR A 318 SHEET 3 AA 3 CYS A 388 LEU A 390 -1 O TYR A 389 N LEU A 310 SHEET 1 AB 3 ASP A 322 ASP A 324 0 SHEET 2 AB 3 VAL A 362 SER A 365 -1 O VAL A 362 N ASP A 324 SHEET 3 AB 3 ALA A 381 LEU A 383 -1 O ALA A 381 N SER A 365 LINK O3' U B 7 P OMU B 8 1555 1555 1.61 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 234 0 1 4 6 0 0 6 0 0 0 13 END