HEADER RNA BINDING PROTEIN 16-OCT-07 2JWN TITLE SOLUTION NMR STRUCTURE OF THE PROTEASE-RESISTENT DOMAIN OF XENOPUS TITLE 2 LAEVIS EPABP2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: EMBRYONIC POLYADENYLATE-BINDING PROTEIN 2-B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PROTEASE-RESISTENT DOMAIN: RESIDUES 60-180; COMPND 5 SYNONYM: EMBRYONIC POLY(A)-BINDING PROTEIN 2-B, EMBRYONIC POLY(A)- COMPND 6 BINDING PROTEIN TYPE II-B, EPABP2-B, XEPABP2-B; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 TISSUE: OOCYTE; SOURCE 6 GENE: EPABP2-B; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVP56K KEYWDS EPABP2, POLY(A) BINDING, STRUCTURAL GENOMICS, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, PSI-2, CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS, KEYWDS 3 CYTOPLASM RNA-BINDING, CESG, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.SONG,J.L.MARKLEY,CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 5 29-MAY-24 2JWN 1 REMARK REVDAT 4 16-MAR-22 2JWN 1 REMARK SEQADV REVDAT 3 02-MAR-10 2JWN 1 JRNL REVDAT 2 24-FEB-09 2JWN 1 VERSN REVDAT 1 30-OCT-07 2JWN 0 JRNL AUTH J.SONG,J.V.MCGIVERN,K.W.NICHOLS,J.L.MARKLEY,M.D.SHEETS JRNL TITL STRUCTURAL BASIS FOR RNA RECOGNITION BY A TYPE II JRNL TITL 2 POLY(A)-BINDING PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 105 15317 2008 JRNL REFN ISSN 0027-8424 JRNL PMID 18824697 JRNL DOI 10.1073/PNAS.0801274105 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH 2.17.0 REMARK 3 AUTHORS : SCHWIETERS, C.D., KUSZEWSKI, J.J., TJANDRA, N., REMARK 3 CLORE, G.M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL OF 4178 REMARK 3 NOE RESTRAINTS (1672 INTRA, 866 SEQUENTIAL, 562 MEDIUM, 912 LONG REMARK 3 RANGE INTERMOLECULAR AND 166 INTERMOLECULAR), 116 HBOND REMARK 3 RESTRAINTS, 326 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS AND 188 N- REMARK 3 H RDC CONSTRAINTS REMARK 4 REMARK 4 2JWN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000100383. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308; 302 REMARK 210 PH : 5.0; 5.0 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 EPABP2-TRP, 100 MM NACL, 10 MM REMARK 210 NAAC, 90% H2O, 10% D2O; 0.5 MM REMARK 210 [U-100% 13C; U-100% 15N] EPABP2- REMARK 210 TRP, 0.5 MM EPABP2-TRP, 100 MM REMARK 210 NACL, 10 MM NAAC, 90% H2O, 10% REMARK 210 D2O; 0.5 MM [U-100% 15N] EPABP2- REMARK 210 TRP, 5 % PEG, 100 MM NACL, 10 MM REMARK 210 NAAC, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H,15N-HSQC; 1H,13C-HSQC; REMARK 210 HNCACB; HCCONH; CBCACONH; REMARK 210 HCCHTOCSY; HBACONH; 13C-EDITED REMARK 210 1H,1H-NOESY; 15C-EDITED 1H,1H- REMARK 210 NOESY; 13C,15N FILTERED, 13C REMARK 210 EDITED 1H,1H-NOESY; 15N IPAP HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DMX; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 3.5, NMRPIPE REMARK 210 97.027.12.56, SPARKY 3.113, REMARK 210 GARANT 2.1, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 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: 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 OE2 GLU A 54 HH TYR B 46 1.54 REMARK 500 OE1 GLU B 20 HZ1 LYS B 31 1.59 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 MET A 6 -170.91 62.90 REMARK 500 1 GLN A 7 -168.26 60.93 REMARK 500 1 ALA A 15 -46.01 76.08 REMARK 500 1 THR A 19 30.84 -161.00 REMARK 500 1 ASN A 43 11.67 57.73 REMARK 500 1 SER A 48 75.60 -100.97 REMARK 500 1 ARG A 113 79.25 43.42 REMARK 500 1 TYR B 18 -79.57 -90.41 REMARK 500 1 THR B 19 99.60 -69.86 REMARK 500 1 ASP B 123 -78.65 -75.86 REMARK 500 2 THR A 14 -79.04 -71.64 REMARK 500 2 ALA A 15 92.26 51.81 REMARK 500 2 ALA A 17 86.28 76.98 REMARK 500 2 TYR A 18 -58.84 -124.79 REMARK 500 2 CYS A 60 -76.56 -94.40 REMARK 500 2 LYS B 12 -64.81 177.43 REMARK 500 2 MET B 13 86.22 63.54 REMARK 500 2 THR B 14 -29.79 171.05 REMARK 500 2 TYR B 18 -66.41 -121.90 REMARK 500 2 TYR B 46 98.52 -69.01 REMARK 500 2 ARG B 113 -79.06 -119.90 REMARK 500 3 GLN A 7 110.42 -165.30 REMARK 500 3 MET A 13 91.18 30.77 REMARK 500 3 ALA A 17 148.58 -173.69 REMARK 500 3 ARG A 113 26.99 -176.53 REMARK 500 3 ASN A 115 -62.19 72.92 REMARK 500 3 ILE A 119 -63.48 -109.53 REMARK 500 3 SER A 120 -87.15 65.94 REMARK 500 3 SER A 121 -173.36 174.22 REMARK 500 3 ASP A 123 -40.04 68.83 REMARK 500 3 THR B 14 -70.46 -112.24 REMARK 500 3 ALA B 15 -42.26 -173.77 REMARK 500 4 PRO A 4 108.46 -49.56 REMARK 500 4 GLN A 7 96.23 -164.60 REMARK 500 4 THR A 9 107.62 -55.06 REMARK 500 4 ALA A 17 75.03 166.60 REMARK 500 4 ASP A 45 106.84 -37.07 REMARK 500 4 TYR A 46 162.81 50.11 REMARK 500 4 SER A 121 109.66 63.55 REMARK 500 4 HIS B 10 -40.84 -135.91 REMARK 500 4 SER B 11 142.30 65.87 REMARK 500 4 GLU B 20 16.35 -59.89 REMARK 500 4 ASN B 43 -19.28 80.96 REMARK 500 5 GLN A 7 76.52 48.81 REMARK 500 5 LYS A 12 -160.39 65.51 REMARK 500 5 TYR A 46 96.44 -64.77 REMARK 500 5 ASP A 98 24.07 -67.57 REMARK 500 5 GLU A 99 -7.81 -156.21 REMARK 500 5 PRO A 117 31.27 -89.77 REMARK 500 5 ILE A 119 99.35 63.42 REMARK 500 REMARK 500 THIS ENTRY HAS 287 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 1 ARG A 65 0.09 SIDE CHAIN REMARK 500 1 ARG B 65 0.09 SIDE CHAIN REMARK 500 4 ARG A 37 0.09 SIDE CHAIN REMARK 500 5 ARG A 65 0.09 SIDE CHAIN REMARK 500 5 ARG B 65 0.09 SIDE CHAIN REMARK 500 15 ARG A 65 0.10 SIDE CHAIN REMARK 500 15 ARG B 65 0.09 SIDE CHAIN REMARK 500 16 ARG A 105 0.09 SIDE CHAIN REMARK 500 17 ARG B 65 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.80182 RELATED DB: TARGETDB DBREF 2JWN A 4 124 UNP Q6TY21 EPA2B_XENLA 60 180 DBREF 2JWN B 4 124 UNP Q6TY21 EPA2B_XENLA 60 180 SEQADV 2JWN ALA A 1 UNP Q6TY21 EXPRESSION TAG SEQADV 2JWN ILE A 2 UNP Q6TY21 EXPRESSION TAG SEQADV 2JWN ALA A 3 UNP Q6TY21 EXPRESSION TAG SEQADV 2JWN ALA B 1 UNP Q6TY21 EXPRESSION TAG SEQADV 2JWN ILE B 2 UNP Q6TY21 EXPRESSION TAG SEQADV 2JWN ALA B 3 UNP Q6TY21 EXPRESSION TAG SEQRES 1 A 124 ALA ILE ALA PRO CYS MET GLN THR THR HIS SER LYS MET SEQRES 2 A 124 THR ALA GLY ALA TYR THR GLU GLY PRO PRO GLN PRO LEU SEQRES 3 A 124 SER ALA GLU GLU LYS LYS GLU ILE ASP LYS ARG SER VAL SEQRES 4 A 124 TYR VAL GLY ASN VAL ASP TYR GLY SER THR ALA GLN ASP SEQRES 5 A 124 LEU GLU ALA HIS PHE SER SER CYS GLY SER ILE ASN ARG SEQRES 6 A 124 ILE THR ILE LEU CYS ASP LYS PHE SER GLY HIS PRO LYS SEQRES 7 A 124 GLY TYR ALA TYR ILE GLU PHE ALA GLU ARG ASN SER VAL SEQRES 8 A 124 ASP ALA ALA VAL ALA MET ASP GLU THR VAL PHE ARG GLY SEQRES 9 A 124 ARG THR ILE LYS VAL LEU PRO LYS ARG THR ASN MET PRO SEQRES 10 A 124 GLY ILE SER SER THR ASP ARG SEQRES 1 B 124 ALA ILE ALA PRO CYS MET GLN THR THR HIS SER LYS MET SEQRES 2 B 124 THR ALA GLY ALA TYR THR GLU GLY PRO PRO GLN PRO LEU SEQRES 3 B 124 SER ALA GLU GLU LYS LYS GLU ILE ASP LYS ARG SER VAL SEQRES 4 B 124 TYR VAL GLY ASN VAL ASP TYR GLY SER THR ALA GLN ASP SEQRES 5 B 124 LEU GLU ALA HIS PHE SER SER CYS GLY SER ILE ASN ARG SEQRES 6 B 124 ILE THR ILE LEU CYS ASP LYS PHE SER GLY HIS PRO LYS SEQRES 7 B 124 GLY TYR ALA TYR ILE GLU PHE ALA GLU ARG ASN SER VAL SEQRES 8 B 124 ASP ALA ALA VAL ALA MET ASP GLU THR VAL PHE ARG GLY SEQRES 9 B 124 ARG THR ILE LYS VAL LEU PRO LYS ARG THR ASN MET PRO SEQRES 10 B 124 GLY ILE SER SER THR ASP ARG HELIX 1 1 SER A 27 ARG A 37 1 11 HELIX 2 2 THR A 49 SER A 59 1 11 HELIX 3 3 GLU A 87 ALA A 96 1 10 HELIX 4 4 SER B 27 ARG B 37 1 11 HELIX 5 5 THR B 49 SER B 59 1 11 HELIX 6 6 GLU B 87 ALA B 96 1 10 SHEET 1 A 9 LYS A 108 PRO A 111 0 SHEET 2 A 9 SER A 38 VAL A 44 -1 N TYR A 40 O LEU A 110 SHEET 3 A 9 LYS A 78 PHE A 85 -1 O ALA A 81 N VAL A 41 SHEET 4 A 9 ILE A 63 ASP A 71 -1 N THR A 67 O TYR A 82 SHEET 5 A 9 ILE B 63 ASP B 71 -1 O ILE B 66 N CYS A 70 SHEET 6 A 9 LYS B 78 PHE B 85 -1 O TYR B 82 N THR B 67 SHEET 7 A 9 SER B 38 ASP B 45 -1 N VAL B 41 O ALA B 81 SHEET 8 A 9 ARG B 105 PRO B 111 -1 O LEU B 110 N TYR B 40 SHEET 9 A 9 THR B 100 PHE B 102 -1 N PHE B 102 O ARG B 105 SHEET 1 B 2 VAL A 101 PHE A 102 0 SHEET 2 B 2 ARG A 105 THR A 106 -1 O ARG A 105 N PHE A 102 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