10 20 30 40 50 60 70 80 2ROK - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA BINDING PROTEIN 28-MAR-08 2ROK
TITLE SOLUTION STRUCTURE OF THE CAP-BINDING DOMAIN OF PARN TITLE 2 COMPLEXED WITH THE CAP ANALOG
COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY(A)-SPECIFIC RIBONUCLEASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CAP-BINDING DOMAIN; COMPND 5 SYNONYM: POLYADENYLATE-SPECIFIC RIBONUCLEASE; COMPND 6 EC: 3.1.13.4; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PARN
KEYWDS RRM, RBD, CAP, STRUCTURAL GENOMICS, RNA BINDING PROTEIN, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR T.NAGATA,S.SUZUKI,R.ENDO,M.SHIROUZU,T.TERADA,M.INOUE, AUTHOR 2 T.KIGAWA,P.GUNTERT,Y.HAYASHIZAKI,Y.MUTO,S.YOKOYAMA,RIKEN AUTHOR 3 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 1 10-FEB-09 2ROK 0
JRNL AUTH T.NAGATA,S.SUZUKI,R.ENDO,M.SHIROUZU,T.TERADA, JRNL AUTH 2 M.INOUE,T.KIGAWA,N.KOBAYASHI,P.GUNTERT,A.TANAKA, JRNL AUTH 3 Y.HAYASHIZAKI,Y.MUTO,S.YOKOYAMA JRNL TITL THE RRM DOMAIN OF POLY(A)-SPECIFIC RIBONUCLEASE JRNL TITL 2 HAS A NONCANONICAL BINDING SITE FOR MRNA CAP JRNL TITL 3 ANALOG RECOGNITION. JRNL REF NUCLEIC ACIDS RES. V. 36 4754 2008 JRNL REFN ISSN 0305-1048 JRNL PMID 18641416 JRNL DOI 10.1093/NAR/GKN458
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2ROK COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-08. REMARK 100 THE RCSB ID CODE IS RCSB150098.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% REMARK 210 15N] PARN, 2.5 MM M7GPPPG, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-13C NOESY, 3D 1H-15N REMARK 210 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 20060702, NMRVIEW REMARK 210 5.0.4, XWINNMR 3.5, KUJIRA REMARK 210 0.9825, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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 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 A 437 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 GLN A 510 47.38 -70.62 REMARK 500 1 SER A 517 -39.62 -145.05 REMARK 500 3 GLN A 510 -48.81 -145.98 REMARK 500 4 LYS A 513 -35.20 -146.63 REMARK 500 4 GLN A 514 29.66 -77.41 REMARK 500 5 SER A 424 -40.17 -153.55 REMARK 500 5 LEU A 433 -3.94 -58.90 REMARK 500 5 LYS A 436 -6.14 -57.74 REMARK 500 5 GLN A 514 6.09 -153.88 REMARK 500 6 SER A 424 -2.40 -140.73 REMARK 500 6 LYS A 436 31.34 -140.41 REMARK 500 6 ASP A 438 -43.07 -156.13 REMARK 500 6 HIS A 439 38.19 -70.26 REMARK 500 6 ASN A 463 17.61 -143.06 REMARK 500 6 ILE A 469 -42.93 -132.89 REMARK 500 6 LYS A 516 -45.77 -146.46 REMARK 500 7 LEU A 433 26.50 -141.80 REMARK 500 7 LYS A 436 11.31 -63.89 REMARK 500 7 GLU A 495 -5.46 -140.55 REMARK 500 7 LYS A 511 19.15 -148.08 REMARK 500 7 GLN A 514 25.48 -73.58 REMARK 500 7 LYS A 516 46.87 -75.88 REMARK 500 8 LYS A 511 20.55 -145.53 REMARK 500 8 SER A 517 -31.76 65.39 REMARK 500 9 SER A 425 35.42 -78.46 REMARK 500 9 ARG A 437 52.04 28.95 REMARK 500 9 GLU A 495 -18.65 52.68 REMARK 500 9 LYS A 511 -18.76 -147.62 REMARK 500 9 LYS A 516 -21.09 -140.94 REMARK 500 10 SER A 424 10.57 -140.41 REMARK 500 10 LEU A 433 17.11 -148.88 REMARK 500 10 GLU A 495 -5.10 -140.43 REMARK 500 10 LYS A 509 84.57 -20.82 REMARK 500 12 SER A 424 10.52 -140.65 REMARK 500 12 SER A 425 25.20 -75.22 REMARK 500 12 ASP A 432 1.40 -63.74 REMARK 500 13 SER A 428 21.97 -143.04 REMARK 500 13 GLN A 434 65.40 37.48 REMARK 500 14 ARG A 437 -12.25 -141.23 REMARK 500 14 ILE A 469 -41.10 -131.72 REMARK 500 14 SER A 517 -51.73 -150.67 REMARK 500 15 GLN A 434 52.58 35.09 REMARK 500 15 ILE A 469 -44.34 -132.68 REMARK 500 15 ASP A 471 1.13 -67.26 REMARK 500 15 GLN A 510 -179.27 55.44 REMARK 500 16 GLU A 495 -7.82 -140.66 REMARK 500 16 GLN A 514 27.58 -157.49 REMARK 500 17 LYS A 436 26.83 -71.30 REMARK 500 17 GLU A 495 -20.68 52.91 REMARK 500 17 LYS A 509 -17.16 -49.85 REMARK 500 18 SER A 496 10.93 -154.95 REMARK 500 19 SER A 427 -0.05 -141.33 REMARK 500 20 SER A 427 -0.17 -141.28 REMARK 500 20 SER A 496 -39.86 -164.46 REMARK 500 20 GLN A 514 37.02 -72.63 REMARK 500 20 SER A 521 -0.76 -143.51 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 7MG A 523 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 524
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WHV RELATED DB: PDB REMARK 900 RELATED ID: MMT007011199.1 RELATED DB: TARGETDB
DBREF 2ROK A 430 516 UNP Q3TUQ8 Q3TUQ8_MOUSE 430 516
SEQADV 2ROK GLY A 423 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK SER A 424 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK SER A 425 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK GLY A 426 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK SER A 427 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK SER A 428 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK GLY A 429 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK SER A 517 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK GLY A 518 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK PRO A 519 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK SER A 520 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK SER A 521 UNP Q3TUQ8 EXPRESSION TAG SEQADV 2ROK GLY A 522 UNP Q3TUQ8 EXPRESSION TAG
SEQRES 1 A 100 GLY SER SER GLY SER SER GLY GLY PRO ASP LEU GLN PRO SEQRES 2 A 100 LYS ARG ASP HIS VAL LEU HIS VAL THR PHE PRO LYS GLU SEQRES 3 A 100 TRP LYS THR SER ASP LEU TYR GLN LEU PHE SER ALA PHE SEQRES 4 A 100 GLY ASN ILE GLN ILE SER TRP ILE ASP ASP THR SER ALA SEQRES 5 A 100 PHE VAL SER LEU SER GLN PRO GLU GLN VAL GLN ILE ALA SEQRES 6 A 100 VAL ASN THR SER LYS TYR ALA GLU SER TYR ARG ILE GLN SEQRES 7 A 100 THR TYR ALA GLU TYR VAL GLY LYS LYS GLN LYS GLY LYS SEQRES 8 A 100 GLN VAL LYS SER GLY PRO SER SER GLY
HET 7MG A 523 39 HET GDP A 524 40
HETNAM 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE
FORMUL 2 7MG C11 H18 N5 O8 P FORMUL 3 GDP C10 H15 N5 O11 P2
HELIX 1 1 LYS A 450 SER A 459 1 10 HELIX 2 2 ALA A 460 GLY A 462 5 3 HELIX 3 3 GLN A 480 SER A 491 1 12 HELIX 4 4 LYS A 492 ALA A 494 5 3 HELIX 5 5 TYR A 502 LYS A 508 1 7 HELIX 6 6 GLY A 518 GLY A 522 5 5
SHEET 1 A 4 GLN A 465 TRP A 468 0 SHEET 2 A 4 SER A 473 SER A 477 -1 O PHE A 475 N SER A 467 SHEET 3 A 4 VAL A 440 THR A 444 -1 N LEU A 441 O VAL A 476 SHEET 4 A 4 ARG A 498 THR A 501 -1 O GLN A 500 N HIS A 442
LINK P 7MG A 523 O3B GDP A 524 1555 1555 1.56
SITE 1 AC1 8 PHE A 445 LYS A 447 TRP A 449 LYS A 450 SITE 2 AC1 8 THR A 451 TRP A 468 ASP A 470 ASP A 471 SITE 1 AC2 5 LYS A 447 TRP A 449 LYS A 450 TRP A 468 SITE 2 AC2 5 ASP A 471
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