PDB Short entry for 2KXN HEADER RNA BINDING PROTEIN/RNA 10-MAY-10 2KXN TITLE NMR STRUCTURE OF HUMAN TRA2BETA1 RRM IN COMPLEX WITH AAGAAC RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*AP*AP*GP*AP*AP*C)-3'; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TRANSFORMER-2 PROTEIN HOMOLOG BETA; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: RRM DOMAIN, RESIDUES 106-200; COMPND 9 SYNONYM: TRA-2 BETA, TRA2-BETA, HTRA2-BETA, TRANSFORMER-2 PROTEIN COMPND 10 HOMOLOG B, SPLICING FACTOR, ARGININE/SERINE-RICH 10; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 GENE: TRA2B, SFRS10; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS SR PROTEIN, RRM, SPLICING FACTOR, RNA PROTEIN COMPLEX, SMN, RNA KEYWDS 2 BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 12 AUTHOR A.CLERY,S.JAYNE,N.BENDERSKA,C.DOMINGUEZ,S.STAMM,F.H.-T.ALLAIN REVDAT 3 05-FEB-20 2KXN 1 REMARK SEQADV REVDAT 2 30-MAY-12 2KXN 1 JRNL VERSN REVDAT 1 16-MAR-11 2KXN 0 JRNL AUTH A.CLERY,S.JAYNE,N.BENDERSKA,C.DOMINGUEZ,S.STAMM,F.H.ALLAIN JRNL TITL MOLECULAR BASIS OF PURINE-RICH RNA RECOGNITION BY THE HUMAN JRNL TITL 2 SR-LIKE PROTEIN TRA2-BETA1 JRNL REF NAT.STRUCT.MOL.BIOL. V. 18 443 2011 JRNL REFN ISSN 1545-9993 JRNL PMID 21399644 JRNL DOI 10.1038/NSMB.2001 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8 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 2KXN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-10. REMARK 100 THE DEPOSITION ID IS D_1000101701. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 120 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-15N] TRA2BETA1-1, 0.8 REMARK 210 MM [U-13C; U-15N] TRA2BETA1-2, REMARK 210 0.8 MM RNA (5'-R(*AP*AP*GP*AP*AP* REMARK 210 C)-3')-3, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-1H NOESY; 3D CBCA(CO)NH; REMARK 210 3D HNCA; 2D 1H-1H TOCSY; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 700 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0, SPARKY 3.113 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 12 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 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 1-12 REMARK 465 RES C SSSEQI REMARK 465 MET B 72 REMARK 465 GLY B 73 REMARK 465 SER B 74 REMARK 465 SER B 75 REMARK 465 HIS B 76 REMARK 465 HIS B 77 REMARK 465 HIS B 78 REMARK 465 HIS B 79 REMARK 465 HIS B 80 REMARK 465 HIS B 81 REMARK 465 SER B 82 REMARK 465 SER B 83 REMARK 465 GLY B 84 REMARK 465 LEU B 85 REMARK 465 VAL B 86 REMARK 465 PRO B 87 REMARK 465 ARG B 88 REMARK 465 GLY B 89 REMARK 465 SER B 90 REMARK 465 HIS B 91 REMARK 465 MET B 92 REMARK 465 ALA B 93 REMARK 465 SER B 94 REMARK 465 MET B 95 REMARK 465 THR B 96 REMARK 465 GLY B 97 REMARK 465 GLY B 98 REMARK 465 GLN B 99 REMARK 465 GLN B 100 REMARK 465 MET B 101 REMARK 465 GLY B 102 REMARK 465 ARG B 103 REMARK 465 GLY B 104 REMARK 465 SER B 105 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 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 A A 5 N9 - C1' - C2' ANGL. DEV. = -7.0 DEGREES REMARK 500 1 A A 5 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 G A 3 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 A A 5 N9 - C1' - C2' ANGL. DEV. = -9.8 DEGREES REMARK 500 2 A A 5 O4' - C1' - N9 ANGL. DEV. = 8.4 DEGREES REMARK 500 3 A A 5 N9 - C1' - C2' ANGL. DEV. = -8.6 DEGREES REMARK 500 3 A A 5 O4' - C1' - N9 ANGL. DEV. = 8.5 DEGREES REMARK 500 4 A A 5 N9 - C1' - C2' ANGL. DEV. = -7.1 DEGREES REMARK 500 4 A A 5 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 5 A A 5 N9 - C1' - C2' ANGL. DEV. = -8.1 DEGREES REMARK 500 5 A A 5 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 6 A A 5 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 7 A A 5 O4' - C1' - N9 ANGL. DEV. = 8.3 DEGREES REMARK 500 8 A A 5 N9 - C1' - C2' ANGL. DEV. = -7.9 DEGREES REMARK 500 8 A A 5 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 9 A A 5 N9 - C1' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 9 A A 5 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 10 A A 5 O4' - C1' - N9 ANGL. DEV. = 7.7 DEGREES REMARK 500 11 A A 5 N9 - C1' - C2' ANGL. DEV. = -7.2 DEGREES REMARK 500 11 A A 5 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 12 A A 4 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 A A 5 N9 - C1' - C2' ANGL. DEV. = -7.4 DEGREES REMARK 500 12 A A 5 O4' - C1' - N9 ANGL. DEV. = 7.5 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 B 117 -23.99 -159.99 REMARK 500 1 LEU B 120 -179.28 -67.75 REMARK 500 1 LEU B 125 31.22 -64.05 REMARK 500 1 SER B 126 -11.54 76.35 REMARK 500 1 GLN B 154 -61.05 -135.69 REMARK 500 1 SER B 155 -154.93 -153.25 REMARK 500 1 ARG B 157 178.32 55.51 REMARK 500 1 LEU B 184 -31.52 -146.87 REMARK 500 1 ASP B 185 13.40 -147.58 REMARK 500 1 ARG B 188 74.37 51.31 REMARK 500 1 ASP B 192 -167.07 174.20 REMARK 500 1 ILE B 195 174.54 128.42 REMARK 500 1 THR B 196 24.66 45.96 REMARK 500 1 LYS B 197 -76.24 36.39 REMARK 500 2 ARG B 111 47.57 -75.85 REMARK 500 2 ALA B 112 15.45 -144.89 REMARK 500 2 PRO B 116 161.50 -49.19 REMARK 500 2 LEU B 120 -169.66 -119.12 REMARK 500 2 LEU B 127 27.31 -67.32 REMARK 500 2 SER B 155 21.36 -157.30 REMARK 500 2 ARG B 157 -149.71 51.20 REMARK 500 2 SER B 158 -136.43 46.58 REMARK 500 2 ARG B 159 -57.83 -127.14 REMARK 500 2 ASN B 168 52.76 -144.73 REMARK 500 2 LEU B 184 -12.64 -140.74 REMARK 500 2 ARG B 188 167.99 66.72 REMARK 500 2 ILE B 195 -37.99 74.18 REMARK 500 2 LYS B 197 -23.73 64.72 REMARK 500 3 HIS B 107 23.94 -144.02 REMARK 500 3 ALA B 112 -85.48 -154.17 REMARK 500 3 ASN B 113 -43.24 -165.53 REMARK 500 3 CYS B 118 42.04 -71.57 REMARK 500 3 LEU B 120 -167.49 -122.24 REMARK 500 3 LEU B 125 19.13 -66.86 REMARK 500 3 SER B 126 38.90 -73.50 REMARK 500 3 LEU B 127 11.56 -58.63 REMARK 500 3 TYR B 151 -169.63 -58.66 REMARK 500 3 ASP B 152 165.70 -45.70 REMARK 500 3 SER B 155 15.19 -69.81 REMARK 500 3 ARG B 156 18.27 58.76 REMARK 500 3 SER B 158 -125.84 4.66 REMARK 500 3 ARG B 159 -68.22 -141.72 REMARK 500 3 ASN B 168 52.39 -142.30 REMARK 500 3 ASP B 171 -16.70 -142.43 REMARK 500 3 LEU B 184 -30.57 -151.58 REMARK 500 3 ASP B 185 20.37 -144.27 REMARK 500 3 ILE B 195 -3.69 67.76 REMARK 500 4 LEU B 120 -167.12 -74.55 REMARK 500 4 LEU B 125 23.05 -77.74 REMARK 500 4 SER B 126 40.54 -82.98 REMARK 500 REMARK 500 THIS ENTRY HAS 185 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 G A 3 0.16 SIDE CHAIN REMARK 500 3 G A 3 0.09 SIDE CHAIN REMARK 500 3 A A 4 0.07 SIDE CHAIN REMARK 500 4 G A 3 0.07 SIDE CHAIN REMARK 500 6 G A 3 0.09 SIDE CHAIN REMARK 500 6 A A 4 0.05 SIDE CHAIN REMARK 500 7 G A 3 0.06 SIDE CHAIN REMARK 500 8 G A 3 0.09 SIDE CHAIN REMARK 500 12 G A 3 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16920 RELATED DB: BMRB DBREF 2KXN B 106 200 UNP P62995 TRA2B_HUMAN 106 200 DBREF 2KXN A 1 6 PDB 2KXN 2KXN 1 6 SEQADV 2KXN MET B 72 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLY B 73 UNP P62995 EXPRESSION TAG SEQADV 2KXN SER B 74 UNP P62995 EXPRESSION TAG SEQADV 2KXN SER B 75 UNP P62995 EXPRESSION TAG SEQADV 2KXN HIS B 76 UNP P62995 EXPRESSION TAG SEQADV 2KXN HIS B 77 UNP P62995 EXPRESSION TAG SEQADV 2KXN HIS B 78 UNP P62995 EXPRESSION TAG SEQADV 2KXN HIS B 79 UNP P62995 EXPRESSION TAG SEQADV 2KXN HIS B 80 UNP P62995 EXPRESSION TAG SEQADV 2KXN HIS B 81 UNP P62995 EXPRESSION TAG SEQADV 2KXN SER B 82 UNP P62995 EXPRESSION TAG SEQADV 2KXN SER B 83 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLY B 84 UNP P62995 EXPRESSION TAG SEQADV 2KXN LEU B 85 UNP P62995 EXPRESSION TAG SEQADV 2KXN VAL B 86 UNP P62995 EXPRESSION TAG SEQADV 2KXN PRO B 87 UNP P62995 EXPRESSION TAG SEQADV 2KXN ARG B 88 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLY B 89 UNP P62995 EXPRESSION TAG SEQADV 2KXN SER B 90 UNP P62995 EXPRESSION TAG SEQADV 2KXN HIS B 91 UNP P62995 EXPRESSION TAG SEQADV 2KXN MET B 92 UNP P62995 EXPRESSION TAG SEQADV 2KXN ALA B 93 UNP P62995 EXPRESSION TAG SEQADV 2KXN SER B 94 UNP P62995 EXPRESSION TAG SEQADV 2KXN MET B 95 UNP P62995 EXPRESSION TAG SEQADV 2KXN THR B 96 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLY B 97 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLY B 98 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLN B 99 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLN B 100 UNP P62995 EXPRESSION TAG SEQADV 2KXN MET B 101 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLY B 102 UNP P62995 EXPRESSION TAG SEQADV 2KXN ARG B 103 UNP P62995 EXPRESSION TAG SEQADV 2KXN GLY B 104 UNP P62995 EXPRESSION TAG SEQADV 2KXN SER B 105 UNP P62995 EXPRESSION TAG SEQRES 1 A 6 A A G A A C SEQRES 1 B 129 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 129 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 B 129 GLY GLN GLN MET GLY ARG GLY SER ARG HIS VAL GLY ASN SEQRES 4 B 129 ARG ALA ASN PRO ASP PRO ASN CYS CYS LEU GLY VAL PHE SEQRES 5 B 129 GLY LEU SER LEU TYR THR THR GLU ARG ASP LEU ARG GLU SEQRES 6 B 129 VAL PHE SER LYS TYR GLY PRO ILE ALA ASP VAL SER ILE SEQRES 7 B 129 VAL TYR ASP GLN GLN SER ARG ARG SER ARG GLY PHE ALA SEQRES 8 B 129 PHE VAL TYR PHE GLU ASN VAL ASP ASP ALA LYS GLU ALA SEQRES 9 B 129 LYS GLU ARG ALA ASN GLY MET GLU LEU ASP GLY ARG ARG SEQRES 10 B 129 ILE ARG VAL ASP PHE SER ILE THR LYS ARG PRO HIS HELIX 1 1 THR B 130 SER B 139 1 10 HELIX 2 2 ASN B 168 ASN B 180 1 13 SHEET 1 A 2 VAL B 122 PHE B 123 0 SHEET 2 A 2 ARG B 190 VAL B 191 -1 O ARG B 190 N PHE B 123 SHEET 1 B 2 ILE B 144 VAL B 150 0 SHEET 2 B 2 PHE B 161 PHE B 166 -1 O PHE B 161 N VAL B 150 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