HEADER RNA BINDING PROTEIN/RNA 09-FEB-17 5X3Z TITLE SOLUTION STRUCTURE OF MUSASHI1 RBD2 IN COMPLEX WITH RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN MUSASHI HOMOLOG 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 109-200; COMPND 5 SYNONYM: MUSASHI-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA (5'-R(*GP*UP*AP*GP*U)-3'); COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MSI1, MSI1H; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_TAXID: 10090 KEYWDS RNA-BINDING PROTEIN, RRM, RBD, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.IWAOKA,T.NAGATA,K.TSUDA,T.IMAI,H.OKANO,N.KOBAYASHI,M.KATAHIRA REVDAT 2 01-MAY-24 5X3Z 1 REMARK REVDAT 1 13-DEC-17 5X3Z 0 JRNL AUTH R.IWAOKA,T.NAGATA,K.TSUDA,T.IMAI,H.OKANO,N.KOBAYASHI, JRNL AUTH 2 M.KATAHIRA JRNL TITL STRUCTURAL INSIGHT INTO THE RECOGNITION OF R(UAG) BY JRNL TITL 2 MUSASHI-1 RBD2, AND CONSTRUCTION OF A MODEL OF MUSASHI-1 JRNL TITL 3 RBD1-2 BOUND TO THE MINIMUM TARGET RNA JRNL REF MOLECULES V. 22 2017 JRNL REFN ESSN 1420-3049 JRNL PMID 28753936 JRNL DOI 10.3390/MOLECULES22071207 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 5X3Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1300002858. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 300 UM [U-100% 13C; U-100% 15N] REMARK 210 MSI1 RBD2, 300 UM RNA (5'-R(*GP* REMARK 210 UP*AP*GP*U)-3'), 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D HNCO; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, NMRVIEW, MAGRO, NMRPIPE REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT 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: 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 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 G B 201 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A B 203 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 G B 204 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.8 DEGREES REMARK 500 2 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 A B 203 N1 - C6 - N6 ANGL. DEV. = -6.8 DEGREES REMARK 500 2 U B 205 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 3 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.5 DEGREES REMARK 500 3 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 A B 203 N1 - C6 - N6 ANGL. DEV. = -7.1 DEGREES REMARK 500 4 ARG A 197 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.6 DEGREES REMARK 500 4 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 A B 203 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 4 G B 204 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 ARG A 148 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 5 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 A B 203 N1 - C6 - N6 ANGL. DEV. = -5.7 DEGREES REMARK 500 6 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 6 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 A B 203 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 7 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 7 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.2 DEGREES REMARK 500 7 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 A B 203 N1 - C6 - N6 ANGL. DEV. = -6.0 DEGREES REMARK 500 7 G B 204 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 8 G B 201 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 8 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 8 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 8 A B 203 N1 - C6 - N6 ANGL. DEV. = -5.6 DEGREES REMARK 500 9 ARG A 148 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 G B 201 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 9 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 9 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 9 A B 203 N1 - C6 - N6 ANGL. DEV. = -5.3 DEGREES REMARK 500 9 G B 204 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 10 ARG A 148 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 150 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 10 A B 203 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 10 A B 203 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 106 ANGLE DEVIATIONS. 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 LYS A 109 46.48 -75.76 REMARK 500 1 ARG A 150 21.23 -72.74 REMARK 500 1 HIS A 170 -58.51 65.19 REMARK 500 1 PRO A 186 36.13 -75.78 REMARK 500 1 LYS A 187 -15.10 59.98 REMARK 500 2 GLU A 130 0.02 -66.61 REMARK 500 2 ARG A 150 5.94 -68.69 REMARK 500 2 HIS A 170 -60.27 65.19 REMARK 500 2 SER A 191 133.70 63.86 REMARK 500 3 LYS A 109 30.19 -71.08 REMARK 500 3 HIS A 170 -56.22 66.84 REMARK 500 4 LYS A 109 37.52 -74.98 REMARK 500 4 HIS A 170 -55.04 65.75 REMARK 500 4 ASN A 176 -0.66 65.05 REMARK 500 5 MET A 108 39.21 -76.89 REMARK 500 5 LYS A 109 38.65 -76.89 REMARK 500 5 HIS A 170 -59.65 65.36 REMARK 500 5 LYS A 187 66.53 -68.85 REMARK 500 5 GLU A 188 -41.54 -146.16 REMARK 500 5 VAL A 189 34.14 -76.90 REMARK 500 6 HIS A 170 -62.21 64.61 REMARK 500 7 HIS A 170 -51.15 66.65 REMARK 500 8 SER A 106 -48.28 -155.79 REMARK 500 8 LYS A 109 30.57 -75.92 REMARK 500 8 ASN A 147 -71.56 -127.37 REMARK 500 8 HIS A 170 -53.36 66.42 REMARK 500 8 ARG A 197 29.27 -152.39 REMARK 500 9 LYS A 109 33.20 -70.69 REMARK 500 9 ASN A 147 -54.66 -135.61 REMARK 500 9 HIS A 170 -58.91 66.22 REMARK 500 9 LYS A 187 44.94 -156.05 REMARK 500 10 HIS A 107 -51.57 -149.90 REMARK 500 10 LYS A 109 46.08 -76.33 REMARK 500 10 HIS A 170 -59.69 64.27 REMARK 500 11 ARG A 150 2.42 -67.33 REMARK 500 11 HIS A 170 -49.82 67.69 REMARK 500 12 LYS A 109 39.87 -75.93 REMARK 500 12 ASN A 147 -64.01 -129.25 REMARK 500 12 HIS A 170 -51.84 66.70 REMARK 500 13 ARG A 150 3.38 -68.62 REMARK 500 13 HIS A 170 -53.22 65.73 REMARK 500 14 HIS A 170 -58.84 65.34 REMARK 500 14 MET A 190 46.53 -75.19 REMARK 500 15 HIS A 107 -73.04 -136.36 REMARK 500 15 LYS A 109 36.28 -74.79 REMARK 500 15 LYS A 144 5.29 -69.22 REMARK 500 15 ASN A 147 -18.28 -140.80 REMARK 500 15 HIS A 170 -48.89 66.04 REMARK 500 15 SER A 191 126.51 65.52 REMARK 500 15 ARG A 199 -55.81 63.04 REMARK 500 REMARK 500 THIS ENTRY HAS 71 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 U B 202 0.08 SIDE CHAIN REMARK 500 2 U B 205 0.06 SIDE CHAIN REMARK 500 5 A B 203 0.10 SIDE CHAIN REMARK 500 6 G B 204 0.05 SIDE CHAIN REMARK 500 6 U B 205 0.06 SIDE CHAIN REMARK 500 7 U B 205 0.06 SIDE CHAIN REMARK 500 8 G B 204 0.08 SIDE CHAIN REMARK 500 10 G B 201 0.08 SIDE CHAIN REMARK 500 18 ARG A 148 0.08 SIDE CHAIN REMARK 500 18 ARG A 150 0.08 SIDE CHAIN REMARK 500 18 A B 203 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36059 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF MUSASHI1 RBD2 IN COMPLEX WITH RNA REMARK 900 RELATED ID: 5X3Y RELATED DB: PDB DBREF 5X3Z A 109 200 UNP Q61474 MSI1H_MOUSE 109 200 DBREF 5X3Z B 201 205 PDB 5X3Z 5X3Z 201 205 SEQADV 5X3Z GLY A 105 UNP Q61474 EXPRESSION TAG SEQADV 5X3Z SER A 106 UNP Q61474 EXPRESSION TAG SEQADV 5X3Z HIS A 107 UNP Q61474 EXPRESSION TAG SEQADV 5X3Z MET A 108 UNP Q61474 EXPRESSION TAG SEQRES 1 A 96 GLY SER HIS MET LYS LYS ILE PHE VAL GLY GLY LEU SER SEQRES 2 A 96 VAL ASN THR THR VAL GLU ASP VAL LYS HIS TYR PHE GLU SEQRES 3 A 96 GLN PHE GLY LYS VAL ASP ASP ALA MET LEU MET PHE ASP SEQRES 4 A 96 LYS THR THR ASN ARG HIS ARG GLY PHE GLY PHE VAL THR SEQRES 5 A 96 PHE GLU SER GLU ASP ILE VAL GLU LYS VAL CYS GLU ILE SEQRES 6 A 96 HIS PHE HIS GLU ILE ASN ASN LYS MET VAL GLU CYS LYS SEQRES 7 A 96 LYS ALA GLN PRO LYS GLU VAL MET SER PRO THR GLY SER SEQRES 8 A 96 ALA ARG GLY ARG SER SEQRES 1 B 5 G U A G U HELIX 1 AA1 THR A 121 GLU A 130 1 10 HELIX 2 AA2 SER A 159 HIS A 170 1 12 HELIX 3 AA3 LYS A 187 SER A 191 5 5 SHEET 1 AA1 5 VAL A 135 PHE A 142 0 SHEET 2 AA1 5 HIS A 149 PHE A 157 -1 O PHE A 154 N MET A 139 SHEET 3 AA1 5 LYS A 110 GLY A 114 -1 N VAL A 113 O GLY A 153 SHEET 4 AA1 5 LYS A 177 LYS A 183 -1 O LYS A 182 N PHE A 112 SHEET 5 AA1 5 PHE A 171 ILE A 174 -1 N HIS A 172 O VAL A 179 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