HEADER TRANSLATION REGULATOR/RNA 07-FEB-14 2MKK TITLE STRUCTURAL MODEL OF TANDEM RRM DOMAINS OF CYTOPLASMIC POLYADENYLATION TITLE 2 ELEMENT BINDING PROTEIN 1 (CPEB1) IN COMPLEX WITH RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOPLASMIC POLYADENYLATION ELEMENT-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 219-430; COMPND 5 SYNONYM: CPE-BP1, CPE-BINDING PROTEIN 1, H-CEBP, HCPEB-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*UP*UP*UP*UP*A)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CPEB1, CPEB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A(+); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES KEYWDS CPEB1, RNA RECOGNITION MOTIF (RRM), CYTOPLASMIC POLYADENYLATION, KEYWDS 2 PROTEIN-RNA INTERACTION, TRANSLATION REGULATION, TRANSLATION KEYWDS 3 REGULATOR-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR T.AFROZ,L.SKRISOVSKA,E.BELLOC,J.G.BOIXET,R.MENDEZ,F.H.-T.ALLAIN REVDAT 1 23-JUL-14 2MKK 0 JRNL AUTH T.AFROZ,L.SKRISOVSKA,E.BELLOC,J.GUILLEN-BOIXET,R.MENDEZ, JRNL AUTH 2 F.H.-T.ALLAIN JRNL TITL A FLY TRAP MECHANISM PROVIDES SEQUENCE-SPECIFIC RNA JRNL TITL 2 RECOGNITION BY CPEB PROTEINS JRNL REF GENES DEV. V. 28 1498 2014 JRNL REFN ISSN 0890-9369 JRNL PMID 24990967 JRNL DOI 10.1101/GAD.241133.114 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MKK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-14. REMARK 100 THE RCSB ID CODE IS RCSB103725. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 0.4-0.6 MM [U-100% 13C; U-100% REMARK 210 15N; U-80% 2H] CPEB1RRM12-1, 0.4- REMARK 210 0.6 MM 5'-UUUUA-3'-2, 100 MM REMARK 210 SODIUM CHLORIDE-3, 50 MM SODIUM REMARK 210 PHOSPHATE-4, 1 MM DTT-5, 1 MM REMARK 210 MAGNESIUM SULFATE-6, 90% H2O/10% REMARK 210 D2O; 0.4-0.6 MM [U-100% 13C; U- REMARK 210 100% 15N] CPEB1RRM12-7, 0.4-0.6 REMARK 210 MM 5'-UUUUA-3'-8, 100 MM SODIUM REMARK 210 CHLORIDE-9, 50 MM SODIUM REMARK 210 PHOSPHATE-10, 1 MM DTT-11, 1 MM REMARK 210 MAGNESIUM SULFATE-12, 90% H2O/10% REMARK 210 D2O; 0.4-0.6 MM [U-100% 13C; U- REMARK 210 100% 15N] CPEB1RRM12-13, 0.4-0.6 REMARK 210 MM 5'-UUUUA-3'-14, 100 MM SODIUM REMARK 210 CHLORIDE-15, 50 MM SODIUM REMARK 210 PHOSPHATE-16, 1 MM DTT-17, 1 MM REMARK 210 MAGNESIUM SULFATE-18, 100% D2O; REMARK 210 0.4-0.6 MM [U-100% 15N] REMARK 210 CPEB1RRM12-19, 0.4-0.6 MM 5'- REMARK 210 UUUUA-3'-20, 100 MM SODIUM REMARK 210 CHLORIDE-21, 50 MM SODIUM REMARK 210 PHOSPHATE-22, 1 MM DTT-23, 1 MM REMARK 210 MAGNESIUM SULFATE-24, 90% H2O/10% REMARK 210 D2O; 0.4-0.6 MM [U-100% 15N] REMARK 210 CPEB1RRM12-25, 0.4-0.6 MM 5'- REMARK 210 UUUUA-3'-26, 100 MM SODIUM REMARK 210 CHLORIDE-27, 50 MM SODIUM REMARK 210 PHOSPHATE-28, 1 MM DTT-29, 1 MM REMARK 210 MAGNESIUM SULFATE-30, 100% D2O; REMARK 210 0.4-0.6 MM [U-100% 15N] REMARK 210 CPEB1RRM12-31, 0.4-0.6 MM 5'- REMARK 210 CUUUA-3'-32, 100 MM SODIUM REMARK 210 CHLORIDE-33, 50 MM SODIUM REMARK 210 PHOSPHATE-34, 1 MM DTT-35, 1 MM REMARK 210 MAGNESIUM SULFATE-36, 100% D2O; REMARK 210 0.4-0.6 MM [U-100% 13C; U-100% REMARK 210 15N] CPEB1RRM12-37, 0.4-0.6 MM 5' REMARK 210 -CUUUA-3'-38, 100 MM SODIUM REMARK 210 CHLORIDE-39, 50 MM SODIUM REMARK 210 PHOSPHATE-40, 1 MM DTT-41, 1 MM REMARK 210 MAGNESIUM SULFATE-42, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D TROSY; 2D 1H- REMARK 210 13C HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 2D 1H-1H TOCSY; 2D 1H- REMARK 210 1H NOESY; 3D TRHNCA; 3D TRHN(CO) REMARK 210 CA; 3D TRCBCA(CO)NH; 3D TRHNCACB; REMARK 210 3D TRHNCACO; 3D TRHNCO; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C NOESY AROMATIC; 2D 13C- REMARK 210 F1-FILTERED F2-FILTERED NOESY; 2D REMARK 210 1H-1H F1-13C-FILTERED F2-13C- REMARK 210 EDITED NOESY; 3D 13C-F1-EDITED REMARK 210 F3-FILTERED NOESY HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ; 600 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CYANA, SPARKY REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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: 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 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 U B 4 O4' - C1' - N1 ANGL. DEV. = 6.2 DEGREES REMARK 500 3 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 4 U B 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 5 U B 3 O4' - C1' - N1 ANGL. DEV. = 5.6 DEGREES REMARK 500 6 U B 1 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 6 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 9 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 10 U B 3 O4' - C1' - N1 ANGL. DEV. = 5.7 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 TRP A 245 33.26 -97.48 REMARK 500 1 GLU A 249 -9.44 -59.07 REMARK 500 1 ASP A 270 19.67 55.16 REMARK 500 1 CYS A 276 59.01 -145.18 REMARK 500 1 HIS A 301 -53.78 -166.51 REMARK 500 1 PRO A 303 32.96 -77.61 REMARK 500 1 ASP A 307 34.78 -76.58 REMARK 500 1 SER A 318 10.46 -147.69 REMARK 500 1 ARG A 322 25.19 -76.07 REMARK 500 1 LEU A 333 1.36 -68.45 REMARK 500 1 ALA A 356 13.46 57.13 REMARK 500 1 PHE A 374 -32.07 -160.14 REMARK 500 1 LYS A 386 -17.34 61.02 REMARK 500 1 PRO A 390 -179.79 -58.46 REMARK 500 1 ILE A 391 154.34 54.82 REMARK 500 1 TYR A 404 -73.98 -59.50 REMARK 500 1 ALA A 411 42.31 -71.60 REMARK 500 1 PHE A 412 0.99 -66.90 REMARK 500 1 LYS A 419 5.18 -150.42 REMARK 500 2 SER A 261 43.16 -81.61 REMARK 500 2 GLU A 287 29.15 -79.39 REMARK 500 2 HIS A 301 -154.43 65.06 REMARK 500 2 PRO A 306 -8.75 -58.72 REMARK 500 2 SER A 318 9.10 -152.87 REMARK 500 2 ARG A 320 -37.16 -148.06 REMARK 500 2 MET A 321 56.01 -142.87 REMARK 500 2 ARG A 322 44.12 -75.67 REMARK 500 2 GLN A 344 -24.32 -142.98 REMARK 500 2 LEU A 357 -22.28 52.22 REMARK 500 2 HIS A 358 -35.21 -171.70 REMARK 500 2 PHE A 374 -26.47 -159.66 REMARK 500 2 LYS A 386 14.90 50.77 REMARK 500 2 PRO A 390 171.12 -46.37 REMARK 500 2 THR A 417 -151.48 -137.57 REMARK 500 2 THR A 418 86.31 -68.92 REMARK 500 3 ASP A 246 44.16 -76.76 REMARK 500 3 THR A 248 -17.33 -142.24 REMARK 500 3 GLU A 249 -25.89 -164.19 REMARK 500 3 HIS A 301 -151.18 63.75 REMARK 500 3 PHE A 314 -167.23 -160.94 REMARK 500 3 ARG A 320 2.10 -69.49 REMARK 500 3 ARG A 322 32.47 -70.72 REMARK 500 3 PHE A 374 -18.98 -147.32 REMARK 500 3 LYS A 386 19.54 49.01 REMARK 500 3 PRO A 390 -113.66 -76.44 REMARK 500 3 ALA A 411 31.71 -91.73 REMARK 500 3 PHE A 412 20.21 -75.71 REMARK 500 3 LYS A 419 -30.70 -135.80 REMARK 500 4 VAL A 243 161.37 52.22 REMARK 500 4 PRO A 244 168.88 -48.86 REMARK 500 REMARK 500 THIS ENTRY HAS 170 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 5 U B 1 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19778 RELATED DB: BMRB REMARK 900 RELATED ID: 2MKE RELATED DB: PDB REMARK 900 RELATED ID: 2MKH RELATED DB: PDB REMARK 900 RELATED ID: 2MKI RELATED DB: PDB REMARK 900 RELATED ID: 2MKJ RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS PROTEIN SEQUENCE IS ISOFORM 4 OF CPEB1_HUMAN. DBREF 2MKK A 219 430 UNP Q9BZB8 CPEB1_HUMAN 219 430 DBREF 2MKK B 1 5 PDB 2MKK 2MKK 1 5 SEQADV 2MKK MET A 218 UNP Q9BZB8 EXPRESSION TAG SEQRES 1 A 213 MET THR TRP SER GLY GLN LEU PRO PRO ARG ASN TYR LYS SEQRES 2 A 213 ASN PRO ILE TYR SER CYS LYS VAL PHE LEU GLY GLY VAL SEQRES 3 A 213 PRO TRP ASP ILE THR GLU ALA GLY LEU VAL ASN THR PHE SEQRES 4 A 213 ARG VAL PHE GLY SER LEU SER VAL GLU TRP PRO GLY LYS SEQRES 5 A 213 ASP GLY LYS HIS PRO ARG CYS PRO PRO LYS GLY TYR VAL SEQRES 6 A 213 TYR LEU VAL PHE GLU LEU GLU LYS SER VAL ARG SER LEU SEQRES 7 A 213 LEU GLN ALA CYS SER HIS ASP PRO LEU SER PRO ASP GLY SEQRES 8 A 213 LEU SER GLU TYR TYR PHE LYS MET SER SER ARG ARG MET SEQRES 9 A 213 ARG CYS LYS GLU VAL GLN VAL ILE PRO TRP VAL LEU ALA SEQRES 10 A 213 ASP SER ASN PHE VAL ARG SER PRO SER GLN ARG LEU ASP SEQRES 11 A 213 PRO SER ARG THR VAL PHE VAL GLY ALA LEU HIS GLY MET SEQRES 12 A 213 LEU ASN ALA GLU ALA LEU ALA ALA ILE LEU ASN ASP LEU SEQRES 13 A 213 PHE GLY GLY VAL VAL TYR ALA GLY ILE ASP THR ASP LYS SEQRES 14 A 213 HIS LYS TYR PRO ILE GLY SER GLY ARG VAL THR PHE ASN SEQRES 15 A 213 ASN GLN ARG SER TYR LEU LYS ALA VAL SER ALA ALA PHE SEQRES 16 A 213 VAL GLU ILE LYS THR THR LYS PHE THR LYS LYS VAL GLN SEQRES 17 A 213 ILE ASP PRO TYR LEU SEQRES 1 B 5 U U U U A HELIX 1 1 GLU A 249 PHE A 256 1 8 HELIX 2 2 PRO A 267 LYS A 272 5 6 HELIX 3 3 LEU A 288 GLN A 297 1 10 HELIX 4 4 ASN A 362 LEU A 373 1 12 HELIX 5 5 ASN A 400 ALA A 411 1 12 SHEET 1 A 5 SER A 263 GLU A 265 0 SHEET 2 A 5 VAL A 282 VAL A 285 -1 O VAL A 285 N SER A 263 SHEET 3 A 5 TYR A 234 LEU A 240 -1 N LEU A 240 O VAL A 282 SHEET 4 A 5 VAL A 326 VAL A 332 -1 O ILE A 329 N PHE A 239 SHEET 5 A 5 TYR A 312 PHE A 314 -1 N TYR A 312 O VAL A 328 SHEET 1 B 5 ASN A 337 PHE A 338 0 SHEET 2 B 5 TYR A 379 THR A 384 -1 O ALA A 380 N PHE A 338 SHEET 3 B 5 GLY A 392 THR A 397 -1 O SER A 393 N ASP A 383 SHEET 4 B 5 THR A 351 GLY A 355 -1 N VAL A 354 O GLY A 394 SHEET 5 B 5 GLN A 425 ASP A 427 -1 O ASP A 427 N PHE A 353 SHEET 1 C 2 ILE A 415 LYS A 416 0 SHEET 2 C 2 THR A 421 LYS A 422 -1 O LYS A 422 N ILE A 415 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