HEADER RNA BINDING PROTEIN/RNA 24-JUN-14 2MQQ TITLE STRUCTURAL INVESTIGATION OF HNRNP L BOUND TO RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENOUS NUCLEAR RIBONUCLEOPROTEIN L; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-245; COMPND 5 SYNONYM: HNRPL PROTEIN, PROTEIN HNRNPL; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*AP*CP*AP*CP*A)-3'); COMPND 9 CHAIN: B, C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: FBLIM1, HNRNP-L, HNRNPL, HNRPL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PTYB11; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS PROTEIN-RNA COMPLEX, RRM, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.BLATTER,F.ALLAIN REVDAT 2 01-MAY-24 2MQQ 1 REMARK REVDAT 1 23-DEC-15 2MQQ 0 JRNL AUTH M.BLATTER,F.ALLAIN JRNL TITL STRUCTURAL INVESTIGATION OF HNRNP L BOUND TO RNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, AMBER REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MQQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000103938. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313.15 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-100% 15N] PROTEIN_1, REMARK 210 3.0 MM RNA (5'-R(*AP*CP*AP*CP*A)- REMARK 210 3'), 60 MM SODIUM CHLORIDE, 40 REMARK 210 MM SODIUM PHOSPHATE, 1 MM DTT, REMARK 210 90% H2O/10% D2O; 1.5 MM [U-100% REMARK 210 13C; U-100% 15N] PROTEIN_1, 3.0 REMARK 210 MM RNA (5'-R(*AP*CP*AP*CP*A)-3'), REMARK 210 60 MM SODIUM CHLORIDE, 40 MM REMARK 210 SODIUM PHOSPHATE, 1 MM DTT, 90% REMARK 210 H2O/10% D2O; 1.5 MM [U-100% 15N] REMARK 210 PROTEIN_1, 3.0 MM RNA (5'-R(*AP* REMARK 210 CP*AP*CP*A)-3'), 60 MM SODIUM REMARK 210 CHLORIDE, 40 MM SODIUM PHOSPHATE, REMARK 210 1 MM DTT, 100% D2O; 1.5 MM [U- REMARK 210 100% 13C; U-100% 15N] PROTEIN_1, REMARK 210 3.0 MM RNA (5'-R(*AP*CP*AP*CP*A)- REMARK 210 3'), 60 MM SODIUM CHLORIDE, 40 REMARK 210 MM SODIUM PHOSPHATE, 1 MM DTT, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-1H NOESY; 2D 1H- REMARK 210 1H TOCSY; 3D F3-FILTERED-F2- REMARK 210 EDITED NOESY; 2D F2-FILTERED REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA 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 : 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 A B 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 A B 1 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 A B 3 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 6 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 8 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 10 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 11 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 12 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 13 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 14 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 14 A C 5 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 15 A B 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 17 A B 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 17 A B 5 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 17 C C 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 19 A B 3 C5' - C4' - C3' ANGL. DEV. = -9.4 DEGREES REMARK 500 19 A B 5 O4' - C1' - N9 ANGL. DEV. = 5.5 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 GLU A 407 -65.36 -121.49 REMARK 500 1 THR A 510 -177.32 -54.73 REMARK 500 1 GLU A 511 -35.24 -28.64 REMARK 500 1 HIS A 561 17.53 57.24 REMARK 500 1 ASN A 568 11.35 -158.11 REMARK 500 2 LEU A 386 28.27 -77.29 REMARK 500 2 GLU A 407 -53.71 -129.06 REMARK 500 2 MET A 446 75.14 -118.96 REMARK 500 2 THR A 510 179.07 -55.25 REMARK 500 2 GLU A 511 -68.80 12.09 REMARK 500 2 ALA A 585 28.33 -145.41 REMARK 500 3 PRO A 374 170.09 -57.40 REMARK 500 3 LEU A 386 32.32 -75.73 REMARK 500 3 GLU A 407 -61.30 -129.93 REMARK 500 3 PHE A 442 15.63 59.92 REMARK 500 3 MET A 446 -152.51 -94.82 REMARK 500 3 THR A 510 -177.29 -54.88 REMARK 500 3 GLU A 511 -33.55 -30.86 REMARK 500 3 HIS A 561 12.62 57.54 REMARK 500 3 ASN A 566 78.02 -155.85 REMARK 500 3 ALA A 585 31.80 -144.62 REMARK 500 4 LEU A 386 27.89 -79.02 REMARK 500 4 THR A 510 -177.21 -54.47 REMARK 500 4 GLU A 511 -41.04 -22.72 REMARK 500 4 ASN A 568 4.57 -152.29 REMARK 500 4 ALA A 585 25.86 -148.49 REMARK 500 5 PRO A 374 171.56 -59.49 REMARK 500 5 LEU A 386 23.13 -78.74 REMARK 500 5 ASP A 387 26.85 -74.24 REMARK 500 5 GLU A 407 -70.68 -119.18 REMARK 500 5 PHE A 440 42.48 -72.85 REMARK 500 5 PHE A 442 8.82 55.92 REMARK 500 5 LYS A 445 150.99 62.99 REMARK 500 5 THR A 510 -177.41 -54.81 REMARK 500 5 GLU A 511 -39.69 -24.46 REMARK 500 5 LYS A 535 -19.44 62.70 REMARK 500 5 HIS A 561 12.78 58.91 REMARK 500 5 ASN A 568 8.78 -160.30 REMARK 500 6 LEU A 386 28.04 -77.97 REMARK 500 6 GLU A 407 -66.89 -132.87 REMARK 500 6 THR A 510 -177.30 -54.82 REMARK 500 6 GLU A 511 -40.35 -24.05 REMARK 500 6 LYS A 535 13.34 49.70 REMARK 500 6 ARG A 538 -10.62 -141.22 REMARK 500 6 HIS A 561 19.28 58.07 REMARK 500 6 ALA A 585 31.49 -143.20 REMARK 500 7 LEU A 386 26.51 -79.03 REMARK 500 7 GLU A 407 -54.65 -139.39 REMARK 500 7 PHE A 442 16.65 58.55 REMARK 500 7 PRO A 458 27.82 -77.77 REMARK 500 REMARK 500 THIS ENTRY HAS 154 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 C C 4 0.07 SIDE CHAIN REMARK 500 3 C C 4 0.06 SIDE CHAIN REMARK 500 4 C C 4 0.07 SIDE CHAIN REMARK 500 5 C C 4 0.08 SIDE CHAIN REMARK 500 7 C C 4 0.07 SIDE CHAIN REMARK 500 8 C C 4 0.07 SIDE CHAIN REMARK 500 12 C C 4 0.08 SIDE CHAIN REMARK 500 13 C C 4 0.07 SIDE CHAIN REMARK 500 15 C C 4 0.06 SIDE CHAIN REMARK 500 17 C C 4 0.07 SIDE CHAIN REMARK 500 19 C C 4 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25043 RELATED DB: BMRB REMARK 900 RELATED ID: 2MQL RELATED DB: PDB REMARK 900 RELATED ID: 2MQM RELATED DB: PDB REMARK 900 RELATED ID: 2MQN RELATED DB: PDB REMARK 900 RELATED ID: 2MQO RELATED DB: PDB REMARK 900 RELATED ID: 2MQP RELATED DB: PDB REMARK 900 RELATED ID: 4QPT RELATED DB: PDB DBREF 2MQQ A 372 586 UNP Q5U1Y5 Q5U1Y5_RAT 31 245 DBREF 2MQQ B 1 5 PDB 2MQQ 2MQQ 1 5 DBREF 2MQQ C 1 5 PDB 2MQQ 2MQQ 1 5 SEQRES 1 A 215 TYR GLY PRO HIS ALA ASP SER PRO VAL LEU MET VAL TYR SEQRES 2 A 215 GLY LEU ASP GLN SER LYS MET ASN CYS ASP ARG VAL PHE SEQRES 3 A 215 ASN VAL PHE CYS LEU TYR GLY ASN VAL GLU LYS VAL LYS SEQRES 4 A 215 PHE MET LYS SER LYS PRO GLY ALA ALA MET VAL GLU MET SEQRES 5 A 215 ALA ASP GLY TYR ALA VAL ASP ARG ALA ILE THR HIS LEU SEQRES 6 A 215 ASN ASN ASN PHE MET PHE GLY GLN LYS MET ASN VAL CYS SEQRES 7 A 215 VAL SER LYS GLN PRO ALA ILE MET PRO GLY GLN SER TYR SEQRES 8 A 215 GLY LEU GLU ASP GLY SER CYS SER TYR LYS ASP PHE SER SEQRES 9 A 215 GLU SER ARG ASN ASN ARG PHE SER THR PRO GLU GLN ALA SEQRES 10 A 215 ALA LYS ASN ARG ILE GLN HIS PRO SER ASN VAL LEU HIS SEQRES 11 A 215 PHE PHE ASN ALA PRO LEU GLU VAL THR GLU GLU ASN PHE SEQRES 12 A 215 PHE GLU ILE CYS ASP GLU LEU GLY VAL LYS ARG PRO THR SEQRES 13 A 215 SER VAL LYS VAL PHE SER GLY LYS SER GLU ARG SER SER SEQRES 14 A 215 SER GLY LEU LEU GLU TRP ASP SER LYS SER ASP ALA LEU SEQRES 15 A 215 GLU THR LEU GLY PHE LEU ASN HIS TYR GLN MET LYS ASN SEQRES 16 A 215 PRO ASN GLY PRO TYR PRO TYR THR LEU LYS LEU CYS PHE SEQRES 17 A 215 SER THR ALA GLN HIS ALA SER SEQRES 1 B 5 A C A C A SEQRES 1 C 5 A C A C A HELIX 1 1 ASN A 392 LEU A 402 1 11 HELIX 2 2 GLY A 426 LEU A 436 1 11 HELIX 3 3 THR A 484 ALA A 489 1 6 HELIX 4 4 THR A 510 LEU A 521 1 12 HELIX 5 5 SER A 548 ASN A 560 1 13 SHEET 1 A 6 ASN A 439 MET A 441 0 SHEET 2 A 6 GLN A 444 VAL A 450 -1 O GLN A 444 N MET A 441 SHEET 3 A 6 VAL A 380 TYR A 384 -1 N MET A 382 O CYS A 449 SHEET 4 A 6 ALA A 418 MET A 423 -1 O VAL A 421 N LEU A 381 SHEET 5 A 6 VAL A 406 MET A 412 -1 N LYS A 410 O MET A 420 SHEET 6 A 6 TYR A 471 ASP A 473 -1 O LYS A 472 N VAL A 409 SHEET 1 B 4 SER A 528 PHE A 532 0 SHEET 2 B 4 SER A 540 GLU A 545 -1 O SER A 541 N PHE A 532 SHEET 3 B 4 VAL A 499 ALA A 505 -1 N LEU A 500 O LEU A 544 SHEET 4 B 4 LYS A 576 PHE A 579 -1 O CYS A 578 N HIS A 501 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