HEADER RNA BINDING PROTEIN 11-JUL-13 4LMZ TITLE STRUCTURAL INSIGHT INTO RNA RECOGNITION BY RRM1+2 DOMAIN OF HUMAN ETR- TITLE 2 3 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*CP*UP*GP*CP*GP*UP*AP*UP*UP*GP*UP*UP*UP*G)- COMPND 3 3'); COMPND 4 CHAIN: B; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CUGBP ELAV-LIKE FAMILY MEMBER 2; COMPND 8 CHAIN: A; COMPND 9 SYNONYM: CELF-2, BRUNO-LIKE PROTEIN 3, CUG TRIPLET REPEAT RNA-BINDING COMPND 10 PROTEIN 2, CUG-BP2, CUG-BP- AND ETR-3-LIKE FACTOR 2, ELAV-TYPE RNA- COMPND 11 BINDING PROTEIN 3, ETR-3, NEUROBLASTOMA APOPTOSIS-RELATED RNA-BINDING COMPND 12 PROTEIN, HNAPOR, RNA-BINDING PROTEIN BRUNOL-3; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 6 ORGANISM_COMMON: HUMAN; SOURCE 7 ORGANISM_TAXID: 9606; SOURCE 8 GENE: CELF2, BRUNOL3, CUGBP2, ETR3, NAPOR; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PET28A KEYWDS CELF FAMILY, ETR-3, GRE, RNA RECOGNITION MOTIF, RNA BINDING, RNA KEYWDS 2 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.BHATT,Y.MANICKAM,N.S.BHAVESH REVDAT 2 20-SEP-23 4LMZ 1 SEQADV REVDAT 1 16-JUL-14 4LMZ 0 JRNL AUTH H.BHATT,Y.MANICKAM,N.S.BHAVESH JRNL TITL SEQUENCE SPECIFIC RNA RECOGNITION OF ETR3 RRM 1-2 DOMAINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5715 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.293 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.660 REMARK 3 FREE R VALUE TEST SET COUNT : 552 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.3273 - 4.4397 1.00 1355 144 0.2218 0.2951 REMARK 3 2 4.4397 - 3.5244 1.00 1283 141 0.2305 0.2540 REMARK 3 3 3.5244 - 3.0790 1.00 1274 132 0.2774 0.3017 REMARK 3 4 3.0790 - 2.7975 1.00 1251 135 0.3191 0.3769 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.004 1507 REMARK 3 ANGLE : 0.874 2054 REMARK 3 CHIRALITY : 0.063 226 REMARK 3 PLANARITY : 0.005 257 REMARK 3 DIHEDRAL : 15.715 576 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.6171 12.5047 -8.0639 REMARK 3 T TENSOR REMARK 3 T11: 0.2933 T22: 0.3086 REMARK 3 T33: 0.2766 T12: 0.0599 REMARK 3 T13: -0.0871 T23: 0.0214 REMARK 3 L TENSOR REMARK 3 L11: -0.1506 L22: -0.0366 REMARK 3 L33: 1.1575 L12: -0.2958 REMARK 3 L13: 0.8602 L23: -0.6195 REMARK 3 S TENSOR REMARK 3 S11: -0.0689 S12: -0.0777 S13: 0.1080 REMARK 3 S21: -0.0520 S22: 0.0574 S23: 0.0871 REMARK 3 S31: -0.7118 S32: -0.4594 S33: 0.0321 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4LMZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JUL-13. REMARK 100 THE DEPOSITION ID IS D_1000080832. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : VARIMAX HR OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5715 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 REMARK 200 RESOLUTION RANGE LOW (A) : 44.322 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: PDB ENTRY 3NMR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, TRIS-HCL, 35% (V/V) 2 REMARK 280 -METHYL 2,4-PENTANDIOL, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 23.50300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.06700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 66.53200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 23.50300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.06700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.53200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 23.50300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 35.06700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 66.53200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 23.50300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 35.06700 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 66.53200 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G B -7 REMARK 465 C B -6 REMARK 465 U B -5 REMARK 465 G B -4 REMARK 465 C B -3 REMARK 465 G B -2 REMARK 465 U B -1 REMARK 465 A B 0 REMARK 465 U B 6 REMARK 465 G B 7 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 62 CG CD1 CD2 REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 LYS A 90 CG CD CE NZ REMARK 470 ASN A 92 CG OD1 ND2 REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 LEU A 129 CG CD1 CD2 REMARK 470 LEU A 135 CG CD1 CD2 REMARK 470 THR A 143 OG1 CG2 REMARK 470 THR A 146 OG1 CG2 REMARK 470 GLN A 151 CG CD OE1 NE2 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 GLN A 11 3.96 85.12 REMARK 500 SER A 17 -166.15 -102.38 REMARK 500 LEU A 135 -156.54 -103.91 REMARK 500 REMARK 500 REMARK: NULL DBREF 4LMZ A 1 176 UNP O95319 CELF2_HUMAN 36 211 DBREF 4LMZ B -7 7 PDB 4LMZ 4LMZ -7 7 SEQADV 4LMZ GLY A -3 UNP O95319 EXPRESSION TAG SEQADV 4LMZ SER A -2 UNP O95319 EXPRESSION TAG SEQADV 4LMZ HIS A -1 UNP O95319 EXPRESSION TAG SEQADV 4LMZ MET A 0 UNP O95319 EXPRESSION TAG SEQRES 1 B 15 G C U G C G U A U U G U U SEQRES 2 B 15 U G SEQRES 1 A 180 GLY SER HIS MET ASP PRO ASP ALA ILE LYS MET PHE VAL SEQRES 2 A 180 GLY GLN ILE PRO ARG SER TRP SER GLU LYS GLU LEU LYS SEQRES 3 A 180 GLU LEU PHE GLU PRO TYR GLY ALA VAL TYR GLN ILE ASN SEQRES 4 A 180 VAL LEU ARG ASP ARG SER GLN ASN PRO PRO GLN SER LYS SEQRES 5 A 180 GLY CYS CYS PHE VAL THR PHE TYR THR ARG LYS ALA ALA SEQRES 6 A 180 LEU GLU ALA GLN ASN ALA LEU HIS ASN ILE LYS THR LEU SEQRES 7 A 180 PRO GLY MET HIS HIS PRO ILE GLN MET LYS PRO ALA ASP SEQRES 8 A 180 SER GLU LYS SER ASN ALA VAL GLU ASP ARG LYS LEU PHE SEQRES 9 A 180 ILE GLY MET VAL SER LYS LYS CYS ASN GLU ASN ASP ILE SEQRES 10 A 180 ARG VAL MET PHE SER PRO PHE GLY GLN ILE GLU GLU CYS SEQRES 11 A 180 ARG ILE LEU ARG GLY PRO ASP GLY LEU SER ARG GLY CYS SEQRES 12 A 180 ALA PHE VAL THR PHE SER THR ARG ALA MET ALA GLN ASN SEQRES 13 A 180 ALA ILE LYS ALA MET HIS GLN SER GLN THR MET GLU GLY SEQRES 14 A 180 CYS SER SER PRO ILE VAL VAL LYS PHE ALA ASP HELIX 1 1 SER A 17 GLU A 26 1 10 HELIX 2 2 PRO A 27 GLY A 29 5 3 HELIX 3 3 THR A 57 HIS A 69 1 13 HELIX 4 4 ASP A 87 LYS A 90 5 4 HELIX 5 5 ALA A 93 ASP A 96 5 4 HELIX 6 6 ASN A 109 SER A 118 1 10 HELIX 7 7 PRO A 119 GLY A 121 5 3 HELIX 8 8 ARG A 147 HIS A 158 1 12 SHEET 1 A 4 VAL A 31 ASP A 39 0 SHEET 2 A 4 GLN A 46 PHE A 55 -1 O GLN A 46 N ASP A 39 SHEET 3 A 4 MET A 7 GLY A 10 -1 N MET A 7 O VAL A 53 SHEET 4 A 4 GLN A 82 PRO A 85 -1 O LYS A 84 N PHE A 8 SHEET 1 B 4 ILE A 123 ARG A 130 0 SHEET 2 B 4 SER A 136 PHE A 144 -1 O THR A 143 N GLU A 124 SHEET 3 B 4 LYS A 98 GLY A 102 -1 N ILE A 101 O ALA A 140 SHEET 4 B 4 VAL A 171 PHE A 174 -1 O LYS A 173 N PHE A 100 CISPEP 1 ASN A 43 PRO A 44 0 -3.82 CISPEP 2 PRO A 75 GLY A 76 0 -1.75 CISPEP 3 GLY A 131 PRO A 132 0 4.19 CRYST1 47.006 70.134 133.064 90.00 90.00 90.00 I 2 2 2 8 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 0.021274 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014258 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007515 0.00000