HEADER RNA BINDING PROTEIN 09-JAN-14 2MJH TITLE SOLUTION STRUCTURE OF THE GLD-1 RNA-BINDING DOMAIN IN COMPLEX WITH RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: FEMALE GERMLINE-SPECIFIC TUMOR SUPPRESSOR GLD-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KH-QUA2 DOMAIN OF GLD-1, UNP RESIDUES 195-336; COMPND 5 SYNONYM: DEFECTIVE IN GERM LINE DEVELOPMENT PROTEIN 1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-CUACUCAUAU-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: GLD-1, T23G11.3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PTYB1; SOURCE 10 OTHER_DETAILS: PURIFICATION VIA THE IMPACT SYSTEM (NEB) THAT RESULTS SOURCE 11 IN THE PROTEIN WITHOUT ANY ADDITIONAL RESIDUES; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES KEYWDS GLD-1, KH-QUA2 DOMAIN, STAR PROTEIN FAMILY, RNA REGULATION, TRA-2, KEYWDS 2 RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.M.DAUBNER,F.H.-T.ALLAIN REVDAT 5 14-JUN-23 2MJH 1 REMARK REVDAT 4 24-JAN-18 2MJH 1 AUTHOR REVDAT 3 30-JUL-14 2MJH 1 JRNL REVDAT 2 02-JUL-14 2MJH 1 JRNL REVDAT 1 28-MAY-14 2MJH 0 JRNL AUTH G.M.DAUBNER,A.BRUMMER,C.TOCCHINI,S.GERHARDY,R.CIOSK, JRNL AUTH 2 M.ZAVOLAN,F.H.ALLAIN JRNL TITL STRUCTURAL AND FUNCTIONAL IMPLICATIONS OF THE QUA2 DOMAIN ON JRNL TITL 2 RNA RECOGNITION BY GLD-1. JRNL REF NUCLEIC ACIDS RES. V. 42 8092 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24838563 JRNL DOI 10.1093/NAR/GKU445 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FF99SB FORCE-FIELD/ IMPLICIT WATER REMARK 4 REMARK 4 2MJH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103687. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.17 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.45 MM [U-15N] GLD-1 (AA 195 REMARK 210 -336), 0.45 MM 5'-CUACUCAUAU-3', REMARK 210 50 MM SODIUM CHLORIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 3 MM DTT, 90% REMARK 210 H2O/10% D2O; 0.45 MM [U-13C; U- REMARK 210 15N] GLD-1 (AA 195-336), 0.45 MM REMARK 210 5'-CUACUCAUAU-3', 50 MM SODIUM REMARK 210 CHLORIDE, 20 MM SODIUM PHOSPHATE, REMARK 210 3 MM DTT, 90% H2O/10% D2O; 0.45 REMARK 210 MM [U-15N] GLD-1 (AA 195-336), REMARK 210 0.45 MM 5'-CUACUCAUAU-3', 50 MM REMARK 210 SODIUM CHLORIDE, 20 MM SODIUM REMARK 210 PHOSPHATE, 3 MM DTT, 100% D2O; REMARK 210 0.45 MM [U-13C; U-15N] GLD-1 (AA REMARK 210 195-336), 0.45 MM 5'-CUACUCAUAU- REMARK 210 3', 50 MM SODIUM CHLORIDE, 20 MM REMARK 210 SODIUM PHOSPHATE, 3 MM DTT, 100% REMARK 210 D2O; 0.45 MM [U-10% 13C; U-100% REMARK 210 15N] GLD-1 (AA 195-336), 0.45 MM REMARK 210 5'-CUACUCAUAU-3', 50 MM SODIUM REMARK 210 CHLORIDE, 20 MM SODIUM PHOSPHATE, REMARK 210 3 MM DTT, 90% H2O/10% D2O; 0.45 REMARK 210 MM [U-15N] GLD-1 (AA 195-336), REMARK 210 0.45 MM 5'-CUACUCAUAU-3', 50 MM REMARK 210 SODIUM CHLORIDE, 20 MM SODIUM REMARK 210 PHOSPHATE, 3 MM DTT, 14 MG/ML REMARK 210 PF1 PHAGE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCO; REMARK 210 3D HN(CA)CO; 3D CBCA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 2D 1H-1H TOCSY; 2D REMARK 210 1H-1H NOESY; 2D F1F F2F 1H-1H REMARK 210 NOESY; 2D F2F 1H-1H NOESY; 3D REMARK 210 F1F F2E 1H-1H NOESY; LONG-RANGE REMARK 210 1H-15N HSQC; 3D HNHA; 2D 1H-15N REMARK 210 IPAP HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 700 MHZ; 750 REMARK 210 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, SPARKY 3.114, TOPSPIN REMARK 210 3.0, TALOS +, PROCHECKNMR 3.5.4, REMARK 210 ATNOSCANDID 2.1, PALES 2.1, WHAT REMARK 210 IF 10.1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 250 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY AND NOE VIOLATIONS 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: 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 C B 21 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 3 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 8 C B 21 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 11 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 12 U B 17 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 15 C B 21 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 17 C B 21 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 18 C B 21 O4' - C1' - N1 ANGL. DEV. = 4.7 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 ALA A 199 -158.63 -97.69 REMARK 500 1 PRO A 212 32.95 -75.28 REMARK 500 1 ARG A 229 25.61 47.95 REMARK 500 1 SER A 256 -3.30 64.09 REMARK 500 1 ALA A 260 15.09 52.41 REMARK 500 1 ARG A 262 87.98 55.49 REMARK 500 1 TRP A 267 35.49 -80.59 REMARK 500 1 GLU A 268 -143.76 54.07 REMARK 500 1 GLU A 284 -8.66 -59.74 REMARK 500 1 MET A 330 179.85 53.51 REMARK 500 2 PRO A 212 32.50 -75.02 REMARK 500 2 LYS A 213 -8.23 -59.08 REMARK 500 2 ARG A 229 23.33 49.13 REMARK 500 2 ARG A 253 -21.54 -145.06 REMARK 500 2 ASP A 254 9.58 -152.33 REMARK 500 2 ARG A 262 28.42 -145.80 REMARK 500 2 GLU A 268 -23.01 -148.57 REMARK 500 2 LEU A 270 2.33 -68.46 REMARK 500 2 PRO A 306 170.92 -56.40 REMARK 500 2 THR A 309 11.14 -141.88 REMARK 500 3 PRO A 212 31.05 -67.46 REMARK 500 3 LYS A 213 -5.42 -59.51 REMARK 500 3 ARG A 229 21.37 49.35 REMARK 500 3 ARG A 253 11.15 -143.19 REMARK 500 3 LYS A 255 -149.92 -147.82 REMARK 500 3 LYS A 257 15.19 -149.61 REMARK 500 3 TRP A 267 22.92 -142.65 REMARK 500 3 ASP A 282 -170.51 -172.75 REMARK 500 4 PRO A 212 34.74 -76.76 REMARK 500 4 ARG A 229 27.38 47.82 REMARK 500 4 ASP A 254 13.74 54.45 REMARK 500 4 ARG A 262 13.44 56.98 REMARK 500 4 TRP A 267 17.68 -141.99 REMARK 500 4 PRO A 306 171.79 -56.03 REMARK 500 4 THR A 309 19.95 -143.22 REMARK 500 4 MET A 330 29.40 46.57 REMARK 500 4 SER A 332 158.01 60.56 REMARK 500 5 PRO A 212 43.24 -82.55 REMARK 500 5 ARG A 229 22.80 49.54 REMARK 500 5 TRP A 267 43.89 -145.96 REMARK 500 5 LEU A 270 37.71 -75.05 REMARK 500 5 THR A 309 -1.88 -141.32 REMARK 500 6 PRO A 212 33.07 -75.33 REMARK 500 6 ARG A 229 23.64 49.32 REMARK 500 6 SER A 251 32.21 -89.68 REMARK 500 6 ALA A 260 15.00 54.56 REMARK 500 6 THR A 309 20.45 -146.66 REMARK 500 6 SER A 332 139.93 62.49 REMARK 500 7 ALA A 199 -142.43 -127.36 REMARK 500 7 ASP A 201 -177.10 63.93 REMARK 500 REMARK 500 THIS ENTRY HAS 167 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19726 RELATED DB: BMRB DBREF 2MJH A 195 336 UNP Q17339 GLD1_CAEEL 195 336 DBREF 2MJH B 16 25 PDB 2MJH 2MJH 16 25 SEQRES 1 A 142 LEU PRO GLU PRO ALA GLY ASP MET ILE SER ILE THR GLU SEQRES 2 A 142 LYS ILE TYR VAL PRO LYS ASN GLU TYR PRO ASP TYR ASN SEQRES 3 A 142 PHE VAL GLY ARG ILE LEU GLY PRO ARG GLY MET THR ALA SEQRES 4 A 142 LYS GLN LEU GLU GLN ASP THR GLY CYS LYS ILE MET VAL SEQRES 5 A 142 ARG GLY LYS GLY SER MET ARG ASP LYS SER LYS GLU SER SEQRES 6 A 142 ALA HIS ARG GLY LYS ALA ASN TRP GLU HIS LEU GLU ASP SEQRES 7 A 142 ASP LEU HIS VAL LEU VAL GLN CYS GLU ASP THR GLU ASN SEQRES 8 A 142 ARG VAL HIS ILE LYS LEU GLN ALA ALA LEU GLU GLN VAL SEQRES 9 A 142 LYS LYS LEU LEU ILE PRO ALA PRO GLU GLY THR ASP GLU SEQRES 10 A 142 LEU LYS ARG LYS GLN LEU MET GLU LEU ALA ILE ILE ASN SEQRES 11 A 142 GLY THR TYR ARG PRO MET LYS SER PRO ASN PRO ALA SEQRES 1 B 10 C U A C U C A U A U HELIX 1 1 ASN A 220 GLY A 227 1 8 HELIX 2 2 GLY A 230 THR A 240 1 11 HELIX 3 3 GLY A 248 MET A 252 5 5 HELIX 4 4 ARG A 286 LEU A 302 1 17 HELIX 5 5 ASP A 310 ASN A 324 1 15 SHEET 1 A 3 MET A 202 TYR A 210 0 SHEET 2 A 3 HIS A 275 THR A 283 -1 O CYS A 280 N ILE A 205 SHEET 3 A 3 LYS A 243 ARG A 247 -1 N MET A 245 O LEU A 277 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