HEADER RNA BINDING PROTEIN 15-MAR-10 2KVI TITLE STRUCTURE OF NAB3 RRM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM DOMAIN; COMPND 5 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, HMD1, YPL190C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS NAB3, RNA-BINDING MOTIF, RRM, TRANSCRIPTION TERMINATION, NUCLEUS, KEYWDS 2 PHOSPHOPROTEIN, RNA-BINDING, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.PERGOLI,K.KUBICEK,F.HOBOR,J.PASULKA,R.STEFL REVDAT 1 17-NOV-10 2KVI 0 JRNL AUTH R.PERGOLI,F.HOBOR,K.KUBICEK,J.PASULKA,R.STEFL JRNL TITL SOLUTION STRUCTURE AND RNA-BINDING STUDY OF RNA-RECOGNITION JRNL TITL 2 MOTIF OF NAB3 JRNL REF J.BIOL.CHEM. 2010 JRNL REFN ESSN 1083-351X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KVI COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB101624. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 8 REMARK 210 IONIC STRENGTH : 0.3 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2.5 MM [U-99% 13C; U-99% 15N] REMARK 210 RNA-BINDING PROTEIN-1, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 3D HCACO; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 2D 1H-13C HSQC; 3D REMARK 210 1H-13C NOESY; 3D 1H-15N NOESY; 3D REMARK 210 HNHA; 3D HCCH-TOCSY; 2D HB(CB) REMARK 210 (CGCD)HD 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, MOLMOL, SPARKY, REMARK 210 TOPSPIN 2.1, NMRPIPE REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A -7 REMARK 465 THR A -6 REMARK 465 GLU A -5 REMARK 465 MET A -4 REMARK 465 HIS A -3 REMARK 465 ASN A -2 REMARK 465 ILE A -1 REMARK 465 PRO A 0 REMARK 465 PRO A 78 REMARK 465 GLN A 79 REMARK 465 PHE A 80 REMARK 465 ASP A 81 REMARK 465 HIS A 82 REMARK 465 GLY A 83 REMARK 465 ASP A 84 REMARK 465 HIS A 85 REMARK 465 GLY A 86 REMARK 465 THR A 87 REMARK 465 ASN A 88 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 PRO A 1 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 1 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 3 PRO A 1 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 4 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 8 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 PRO A 1 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 9 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 12 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 13 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 13 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 13 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 14 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 14 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 14 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 16 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 16 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 17 PRO A 1 CA - N - CD ANGL. DEV. = -8.7 DEGREES REMARK 500 17 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 18 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 20 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.5 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 ASN A 9 -17.29 61.80 REMARK 500 1 PRO A 11 35.43 -82.48 REMARK 500 1 ILE A 30 151.74 57.43 REMARK 500 1 MET A 31 -71.08 -136.05 REMARK 500 1 ASN A 37 -164.05 63.73 REMARK 500 1 ALA A 38 30.13 -70.39 REMARK 500 1 ASN A 46 124.71 58.85 REMARK 500 1 SER A 58 -83.20 -92.38 REMARK 500 1 LYS A 65 28.45 46.40 REMARK 500 1 LYS A 66 -47.72 -140.32 REMARK 500 2 LEU A 10 -45.97 -134.99 REMARK 500 2 PRO A 11 21.27 -73.14 REMARK 500 2 ILE A 30 148.78 62.33 REMARK 500 2 MET A 31 -96.88 -131.99 REMARK 500 2 ASN A 34 70.41 -154.15 REMARK 500 2 ASN A 37 -170.37 56.29 REMARK 500 2 ALA A 38 1.79 -68.82 REMARK 500 2 PHE A 39 59.62 -144.04 REMARK 500 2 ASN A 46 148.84 62.26 REMARK 500 2 ASN A 62 -46.75 -147.98 REMARK 500 3 PRO A 11 42.70 -65.23 REMARK 500 3 ILE A 30 155.31 62.00 REMARK 500 3 MET A 31 -65.09 -139.76 REMARK 500 3 ASN A 37 -159.64 58.12 REMARK 500 3 ASN A 46 128.92 58.51 REMARK 500 4 LEU A 10 -52.91 -146.97 REMARK 500 4 ILE A 30 154.09 61.18 REMARK 500 4 MET A 31 -59.70 -145.43 REMARK 500 4 ASN A 37 -124.04 44.44 REMARK 500 4 ASN A 46 124.27 56.38 REMARK 500 4 GLU A 57 -62.41 -97.63 REMARK 500 4 LYS A 65 -4.38 -146.92 REMARK 500 5 LEU A 10 -51.56 -128.51 REMARK 500 5 ILE A 30 154.18 64.27 REMARK 500 5 MET A 31 -65.70 -134.62 REMARK 500 5 ASN A 37 -140.19 55.84 REMARK 500 5 ASN A 46 145.17 67.47 REMARK 500 5 SER A 73 -155.69 -86.49 REMARK 500 5 SER A 74 38.81 -68.07 REMARK 500 6 ASN A 9 90.46 -63.92 REMARK 500 6 LEU A 10 -48.69 -153.24 REMARK 500 6 ILE A 30 155.54 60.06 REMARK 500 6 MET A 31 -65.02 -137.86 REMARK 500 6 ASN A 37 -160.06 60.09 REMARK 500 6 ASN A 46 139.22 54.24 REMARK 500 6 GLU A 60 13.10 56.44 REMARK 500 6 LYS A 66 -39.24 -144.71 REMARK 500 6 SER A 74 6.22 -69.72 REMARK 500 7 ASN A 9 41.02 -74.38 REMARK 500 7 ILE A 30 158.18 58.66 REMARK 500 REMARK 500 THIS ENTRY HAS 179 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 6 ARG A 22 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L41 RELATED DB: PDB REMARK 900 NAB3 RRM - UCUU COMPLEX REMARK 900 RELATED ID: 16567 RELATED DB: BMRB DBREF 2KVI A -6 88 UNP P38996 NAB3_YEAST 321 415 SEQADV 2KVI MET A -7 UNP P38996 INITIATING METHIONINE SEQRES 1 A 96 MET THR GLU MET HIS ASN ILE PRO PRO LYS SER ARG LEU SEQRES 2 A 96 PHE ILE GLY ASN LEU PRO LEU LYS ASN VAL SER LYS GLU SEQRES 3 A 96 ASP LEU PHE ARG ILE PHE SER PRO TYR GLY HIS ILE MET SEQRES 4 A 96 GLN ILE ASN ILE LYS ASN ALA PHE GLY PHE ILE GLN PHE SEQRES 5 A 96 ASP ASN PRO GLN SER VAL ARG ASP ALA ILE GLU CYS GLU SEQRES 6 A 96 SER GLN GLU MET ASN PHE GLY LYS LYS LEU ILE LEU GLU SEQRES 7 A 96 VAL SER SER SER ASN ALA ARG PRO GLN PHE ASP HIS GLY SEQRES 8 A 96 ASP HIS GLY THR ASN HELIX 1 1 SER A 16 SER A 25 1 10 HELIX 2 2 ASN A 46 SER A 58 1 13 SHEET 1 A 4 GLN A 32 LYS A 36 0 SHEET 2 A 4 PHE A 39 PHE A 44 -1 O GLN A 43 N GLN A 32 SHEET 3 A 4 SER A 3 GLY A 8 -1 N LEU A 5 O ILE A 42 SHEET 4 A 4 LEU A 69 SER A 73 -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 MODEL 1