HEADER RNA BINDING PROTEIN/RNA 01-SEP-14 2MTV TITLE SOLUTION STRUCTURE OF THE YTH DOMAIN OF YT521-B IN COMPLEX WITH N6- TITLE 2 METHYLADENOSINE CONTAINING RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 347-502; COMPND 5 SYNONYM: PUTATIVE SPLICING FACTOR YT521, RA301-BINDING PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA_(5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3'); COMPND 9 CHAIN: B; 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: YTHDC1, YT521; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTYB11; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS YTH, M6A, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.THELER,C.DOMINGUEZ,M.BLATTER,J.BOUDET,F.H.-T.ALLAIN REVDAT 2 31-DEC-14 2MTV 1 JRNL REVDAT 1 26-NOV-14 2MTV 0 JRNL AUTH D.THELER,C.DOMINGUEZ,M.BLATTER,J.BOUDET,F.H.ALLAIN JRNL TITL SOLUTION STRUCTURE OF THE YTH DOMAIN IN COMPLEX WITH JRNL TITL 2 N6-METHYLADENOSINE RNA: A READER OF METHYLATED RNA. JRNL REF NUCLEIC ACIDS RES. V. 42 13911 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 25389274 JRNL DOI 10.1093/NAR/GKU1116 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 2MTV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-SEP-14. REMARK 100 THE RCSB ID CODE IS RCSB104038. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN_1, 0.8 MM RNA (5'-R(*UP* REMARK 210 GP*(6MZ)P*CP*AP*C)-3'), 25 MM REMARK 210 SODIUM PHOSPHATE, 25 MM SODIUM REMARK 210 CHLORIDE, 10 MM BETA- REMARK 210 MERCAPTOETHANOL, 90% H2O/10% D2O; REMARK 210 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN_1, 0.8 MM RNA (5'-R(*UP* REMARK 210 GP*(6MZ)P*CP*AP*C)-3'), 25 MM REMARK 210 SODIUM PHOSPHATE, 25 MM SODIUM REMARK 210 CHLORIDE, 10 MM BETA- REMARK 210 MERCAPTOETHANOL, 100% D2O; 0.8 MM REMARK 210 [U-99% 15N] PROTEIN_1, 0.8 MM RNA REMARK 210 (5'-R(*UP*GP*(6MZ)P*CP*AP*C)-3'), REMARK 210 25 MM SODIUM PHOSPHATE, 25 MM REMARK 210 SODIUM CHLORIDE, 10 MM BETA- REMARK 210 MERCAPTOETHANOL, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N 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 CBCA(CO)NH; 3D HNCO; REMARK 210 3D HNCA; 3D HNCACB; 3D H(CCO)NH; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D C(CO)NH; 2D 1H -1H REMARK 210 NOESY 13C F1-FILTERED F2- REMARK 210 FILTERED; 3D 1H-13C NOESY 13C F1- REMARK 210 EDITED F3-FILTERED; 2D 1H -1H REMARK 210 NOESY 13C15N F2-FILTERED 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 : SPARKY, TALOS, TOPSPIN, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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 G B 2 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 2 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 3 G B 2 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 5 G B 2 O4' - C1' - N9 ANGL. DEV. = 7.5 DEGREES REMARK 500 6 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 6 C B 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 8 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 8 C B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.6 DEGREES REMARK 500 10 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 11 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 12 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 12 C B 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 13 G B 2 O4' - C1' - N9 ANGL. DEV. = 7.0 DEGREES REMARK 500 13 C B 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 14 C B 4 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 15 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 16 G B 2 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 17 G B 2 O4' - C1' - N9 ANGL. DEV. = 7.2 DEGREES REMARK 500 18 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 18 C B 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 19 G B 2 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 20 G B 2 O4' - C1' - N9 ANGL. DEV. = 7.3 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 SER A 349 -165.46 55.50 REMARK 500 1 ASP A 357 -4.50 -147.15 REMARK 500 1 LEU A 442 -166.29 -108.90 REMARK 500 1 GLU A 470 29.78 -72.14 REMARK 500 1 HIS A 471 17.03 56.64 REMARK 500 2 SER A 349 -165.54 -69.32 REMARK 500 2 LYS A 350 -7.91 -57.48 REMARK 500 2 LEU A 442 -164.97 -106.96 REMARK 500 2 GLU A 470 37.71 -75.09 REMARK 500 2 HIS A 471 15.45 56.93 REMARK 500 3 SER A 349 -162.35 56.11 REMARK 500 3 ASP A 357 -4.15 -146.81 REMARK 500 3 HIS A 424 3.98 -155.83 REMARK 500 3 LEU A 442 -166.17 -114.20 REMARK 500 3 GLU A 470 33.64 -79.22 REMARK 500 3 HIS A 471 14.93 56.82 REMARK 500 4 THR A 348 5.45 -65.50 REMARK 500 4 LYS A 350 -26.93 -151.62 REMARK 500 4 LEU A 442 -164.01 -107.00 REMARK 500 4 ASN A 469 -159.63 -148.67 REMARK 500 4 GLU A 470 21.04 -73.93 REMARK 500 4 HIS A 471 15.07 57.94 REMARK 500 5 LYS A 350 -22.51 60.44 REMARK 500 5 LEU A 442 -166.10 -114.83 REMARK 500 5 GLU A 470 27.23 -71.86 REMARK 500 5 HIS A 471 18.26 56.42 REMARK 500 5 ASP A 498 31.65 -77.81 REMARK 500 6 SER A 349 -56.01 -157.24 REMARK 500 6 LEU A 442 -165.32 -112.41 REMARK 500 6 ASN A 469 -158.32 -145.42 REMARK 500 6 GLU A 470 22.67 -73.77 REMARK 500 6 HIS A 471 14.82 57.86 REMARK 500 7 SER A 349 -165.16 54.67 REMARK 500 7 LEU A 442 -163.79 -105.48 REMARK 500 7 GLU A 470 21.22 -72.85 REMARK 500 7 HIS A 471 15.11 57.46 REMARK 500 8 THR A 348 -66.44 59.69 REMARK 500 8 SER A 349 -117.15 52.55 REMARK 500 8 LEU A 442 -166.35 -111.32 REMARK 500 8 GLU A 470 32.26 -72.37 REMARK 500 8 HIS A 471 17.81 56.16 REMARK 500 9 SER A 349 -161.51 55.28 REMARK 500 9 HIS A 424 3.34 -160.69 REMARK 500 9 LEU A 442 -166.57 -105.71 REMARK 500 9 ASN A 469 -155.32 -139.68 REMARK 500 9 GLU A 470 21.39 -73.43 REMARK 500 9 HIS A 471 13.92 57.51 REMARK 500 9 PRO A 473 150.64 -49.72 REMARK 500 10 SER A 349 -59.91 -155.37 REMARK 500 10 LEU A 442 -168.25 -111.23 REMARK 500 REMARK 500 THIS ENTRY HAS 110 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 7 THR A 348 23.9 L L OUTSIDE RANGE REMARK 500 8 THR A 348 24.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25188 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AUTHOR STATED THAT T253S IS NOT A MUTATION BUT A CONFLICT IN UNP. DBREF 2MTV A 347 502 UNP Q9QY02 YTDC1_RAT 347 502 DBREF 2MTV B 1 6 PDB 2MTV 2MTV 1 6 SEQADV 2MTV SER A 353 UNP Q9QY02 TYR 353 CONFLICT SEQRES 1 A 156 GLN THR SER LYS LEU LYS SER VAL LEU GLN ASP ALA ARG SEQRES 2 A 156 PHE PHE LEU ILE LYS SER ASN ASN HIS GLU ASN VAL SER SEQRES 3 A 156 LEU ALA LYS ALA LYS GLY VAL TRP SER THR LEU PRO VAL SEQRES 4 A 156 ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SER ALA ARG SEQRES 5 A 156 SER VAL ILE LEU ILE PHE SER VAL ARG GLU SER GLY LYS SEQRES 6 A 156 PHE GLN GLY PHE ALA ARG LEU SER SER GLU SER HIS HIS SEQRES 7 A 156 GLY GLY SER PRO ILE HIS TRP VAL LEU PRO ALA GLY MET SEQRES 8 A 156 SER ALA LYS MET LEU GLY GLY VAL PHE LYS ILE ASP TRP SEQRES 9 A 156 ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SER ALA HIS SEQRES 10 A 156 LEU THR ASN PRO TRP ASN GLU HIS LYS PRO VAL LYS ILE SEQRES 11 A 156 GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU CYS GLY THR SEQRES 12 A 156 GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SER ILE ASP SEQRES 1 B 6 U G 6MZ C A C MODRES 2MTV 6MZ B 3 A N6-METHYLADENOSINE-5'-MONOPHOSPHATE HET 6MZ B 3 36 HETNAM 6MZ N6-METHYLADENOSINE-5'-MONOPHOSPHATE FORMUL 2 6MZ C11 H16 N5 O7 P HELIX 1 1 THR A 348 LYS A 350 5 3 HELIX 2 2 LEU A 351 GLN A 356 1 6 HELIX 3 3 ASN A 367 GLY A 378 1 12 HELIX 4 4 LEU A 383 ALA A 397 1 15 HELIX 5 5 SER A 438 LEU A 442 5 5 HELIX 6 6 PRO A 457 SER A 461 5 5 HELIX 7 7 GLU A 484 PHE A 495 1 12 HELIX 8 8 ASP A 498 ASP A 502 5 5 SHEET 1 A 6 VAL A 379 TRP A 380 0 SHEET 2 A 6 PHE A 446 CYS A 452 -1 O PHE A 446 N TRP A 380 SHEET 3 A 6 PHE A 412 LEU A 418 -1 N ARG A 417 O ASP A 449 SHEET 4 A 6 VAL A 400 SER A 405 -1 N LEU A 402 O ALA A 416 SHEET 5 A 6 ARG A 359 ILE A 363 1 N PHE A 361 O ILE A 403 SHEET 6 A 6 GLN A 481 ILE A 483 -1 O GLN A 481 N LEU A 362 LINK O3' G B 2 P 6MZ B 3 1555 1555 1.61 LINK O3' 6MZ B 3 P C B 4 1555 1555 1.61 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