PDB Short entry for 2L41 HEADER RNA BINDING PROTEIN/RNA 28-SEP-10 2L41 TITLE NAB3 RRM - UCUU COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RRM DOMAIN FROM NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN COMPND 3 3; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: RRM DOMAIN FROM NAB3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(P*UP*CP*UP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: NAB3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET22B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS NAB3 RRM, UCUU OLIGONUCLEOTIDE, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.STEFL,R.PERGOLI,F.HOBOR,K.KUBICEK,M.ZIMMERMANN,J.PASULKA,C.HOFR REVDAT 3 30-MAY-12 2L41 1 JRNL VERSN REVDAT 2 24-NOV-10 2L41 1 REMARK REVDAT 1 17-NOV-10 2L41 0 JRNL AUTH F.HOBOR,R.PERGOLI,K.KUBICEK,D.HROSSOVA,V.BACIKOVA, JRNL AUTH 2 M.ZIMMERMANN,J.PASULKA,C.HOFR,S.VANACOVA,R.STEFL JRNL TITL RECOGNITION OF TRANSCRIPTION TERMINATION SIGNAL BY THE JRNL TITL 2 NUCLEAR POLYADENYLATED RNA-BINDING (NAB) 3 PROTEIN JRNL REF J.BIOL.CHEM. V. 286 3645 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21084293 JRNL DOI 10.1074/JBC.M110.158774 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES REFINED IN EXPLICIT SOLVENT REMARK 4 REMARK 4 2L41 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-OCT-10. REMARK 100 THE RCSB ID CODE IS RCSB101929. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2.5MM [U-99% 13C; U-99% 15N] REMARK 210 NAB3 RRM-1, 2.5MM RNA-2, 50MM REMARK 210 SODIUM PHOSPHATE BUFFER(PH 7.5)- REMARK 210 3, 150MM SODIUM CHLORIDE-4, 10MM REMARK 210 BETA-MERCAPTOETHANOL-5, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H TOCSY; REMARK 210 3D HNCA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HNHA; 3D HCCH-TOCSY; 2D REMARK 210 HB(CB)(CGCD)HD; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N NOESY; 2D F1 FILTERED REMARK 210 F2 FILTERED; 2D F1 FILTERED F2 REMARK 210 EDITED REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, TOPSPIN 2.1, SPARKY REMARK 210 3.0, MOLMOL, AMBER 10, WHATIF REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 1 U B 81 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 U B 81 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 2 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 PRO A 1 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 3 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 C B 79 N1 - C2 - O2 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 C B 79 N3 - C2 - O2 ANGL. DEV. = -5.2 DEGREES REMARK 500 4 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 4 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 C B 79 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 C B 79 N3 - C2 - O2 ANGL. DEV. = -5.1 DEGREES REMARK 500 6 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 C B 79 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 6 U B 81 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 6 U B 81 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 7 PRO A 1 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 7 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 C B 79 N3 - C2 - O2 ANGL. DEV. = -4.3 DEGREES REMARK 500 7 U B 81 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 8 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 C B 79 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 9 PRO A 1 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 9 C B 79 N3 - C2 - O2 ANGL. DEV. = -4.6 DEGREES REMARK 500 10 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 C B 79 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 11 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 U B 78 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 11 C B 79 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 12 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 C B 79 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 13 PRO A 1 CA - N - CD ANGL. DEV. = -10.2 DEGREES REMARK 500 13 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 U B 81 O4' - C1' - N1 ANGL. DEV. = 5.5 DEGREES REMARK 500 13 U B 81 N3 - C2 - O2 ANGL. DEV. = -4.9 DEGREES REMARK 500 14 PRO A 1 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 14 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 U B 78 O4' - C1' - N1 ANGL. DEV. = 6.6 DEGREES REMARK 500 14 U B 80 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 15 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 U B 78 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 65 ANGLE DEVIATIONS. 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 LYS A 13 31.58 -153.27 REMARK 500 1 ASN A 14 146.78 58.42 REMARK 500 1 ILE A 23 -76.98 -60.73 REMARK 500 1 SER A 25 -41.47 -157.90 REMARK 500 1 PRO A 26 43.44 -81.01 REMARK 500 1 ILE A 30 167.69 62.22 REMARK 500 1 MET A 31 -71.59 -152.12 REMARK 500 1 ASN A 46 86.79 66.60 REMARK 500 1 SER A 73 34.18 -77.43 REMARK 500 1 ASN A 75 37.62 -79.12 REMARK 500 2 ASN A 9 98.03 -51.03 REMARK 500 2 LEU A 10 -56.64 -150.11 REMARK 500 2 LEU A 12 -15.07 57.02 REMARK 500 2 ASN A 14 29.13 44.61 REMARK 500 2 ILE A 23 -75.05 -64.14 REMARK 500 2 SER A 25 -49.76 -155.61 REMARK 500 2 MET A 31 -67.56 -162.03 REMARK 500 2 ASN A 46 78.59 61.87 REMARK 500 2 GLU A 57 -55.39 -137.23 REMARK 500 2 GLU A 60 37.29 -79.71 REMARK 500 2 LYS A 66 -37.70 -136.77 REMARK 500 3 ASN A 9 30.70 -78.16 REMARK 500 3 LEU A 10 66.75 33.14 REMARK 500 3 ASN A 14 96.40 -12.49 REMARK 500 3 ILE A 23 -79.51 -60.87 REMARK 500 3 SER A 25 -30.46 -135.09 REMARK 500 3 ILE A 30 158.61 63.56 REMARK 500 3 MET A 31 -79.79 -151.72 REMARK 500 3 ALA A 38 -56.68 -144.46 REMARK 500 3 ASN A 46 76.79 67.63 REMARK 500 4 LEU A 10 66.74 38.45 REMARK 500 4 LEU A 12 32.68 -81.40 REMARK 500 4 ILE A 23 -73.19 -63.36 REMARK 500 4 SER A 25 -31.36 -162.48 REMARK 500 4 MET A 31 -57.88 -166.08 REMARK 500 4 ASN A 37 39.50 -72.79 REMARK 500 4 ALA A 38 -43.64 -153.82 REMARK 500 4 ASN A 46 105.34 69.69 REMARK 500 4 SER A 58 23.53 -72.55 REMARK 500 5 ASN A 9 -162.98 -64.48 REMARK 500 5 ILE A 23 -77.20 -65.26 REMARK 500 5 SER A 25 -29.88 -158.66 REMARK 500 5 MET A 31 -73.09 -159.84 REMARK 500 5 ALA A 38 -53.87 64.87 REMARK 500 5 ASN A 46 92.24 66.51 REMARK 500 5 SER A 58 35.78 -72.63 REMARK 500 6 LEU A 10 72.53 43.08 REMARK 500 6 LEU A 12 32.15 -78.18 REMARK 500 6 LYS A 13 -56.61 -146.71 REMARK 500 6 ILE A 23 -76.73 -66.22 REMARK 500 REMARK 500 THIS ENTRY HAS 191 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 2 C B 79 0.10 SIDE CHAIN REMARK 500 6 C B 79 0.07 SIDE CHAIN REMARK 500 7 U B 78 0.07 SIDE CHAIN REMARK 500 7 U B 81 0.07 SIDE CHAIN REMARK 500 8 ARG A 51 0.08 SIDE CHAIN REMARK 500 9 U B 78 0.07 SIDE CHAIN REMARK 500 10 ARG A 51 0.08 SIDE CHAIN REMARK 500 11 C B 79 0.07 SIDE CHAIN REMARK 500 13 C B 79 0.07 SIDE CHAIN REMARK 500 14 C B 79 0.09 SIDE CHAIN REMARK 500 14 U B 81 0.07 SIDE CHAIN REMARK 500 15 C B 79 0.07 SIDE CHAIN REMARK 500 17 C B 79 0.11 SIDE CHAIN REMARK 500 17 U B 81 0.10 SIDE CHAIN REMARK 500 20 C B 79 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KVI RELATED DB: PDB DBREF 2L41 A 1 77 UNP P38996 NAB3_YEAST 328 404 DBREF 2L41 B 78 81 PDB 2L41 2L41 78 81 SEQRES 1 A 77 PRO LYS SER ARG LEU PHE ILE GLY ASN LEU PRO LEU LYS SEQRES 2 A 77 ASN VAL SER LYS GLU ASP LEU PHE ARG ILE PHE SER PRO SEQRES 3 A 77 TYR GLY HIS ILE MET GLN ILE ASN ILE LYS ASN ALA PHE SEQRES 4 A 77 GLY PHE ILE GLN PHE ASP ASN PRO GLN SER VAL ARG ASP SEQRES 5 A 77 ALA ILE GLU CYS GLU SER GLN GLU MET ASN PHE GLY LYS SEQRES 6 A 77 LYS LEU ILE LEU GLU VAL SER SER SER ASN ALA ARG SEQRES 1 B 4 U C U U HELIX 1 1 SER A 16 PHE A 24 1 9 HELIX 2 2 ASN A 46 SER A 58 1 13 SHEET 1 A 4 GLN A 32 ASN A 34 0 SHEET 2 A 4 PHE A 41 PHE A 44 -1 O GLN A 43 N GLN A 32 SHEET 3 A 4 SER A 3 ILE A 7 -1 N LEU A 5 O ILE A 42 SHEET 4 A 4 LEU A 69 SER A 72 -1 O SER A 72 N ARG A 4 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