HEADER IMMUNE SYSTEM/RNA 24-AUG-00 1FNX TITLE SOLUTION STRUCTURE OF THE HUC RBD1-RBD2 COMPLEXED WITH THE AU-RICH TITLE 2 ELEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: AU-RICH RNA ELEMENT; COMPND 3 CHAIN: R; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: RNA DECAMER; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HU ANTIGEN C; COMPND 8 CHAIN: H; COMPND 9 FRAGMENT: THE FIRST AND THE SECOND RNA-BINDING DOMAINS; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 5 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 6 ORGANISM_TAXID: 10090; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA-BINDING DOMAIN, PROTEIN-RNA COMPLEX, IMMUNE SYSTEM-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR M.INOUE,M.HIRAO,K.KASASHIMA,I.-S.KIM,G.KAWAI,T.KIGAWA,H.SAKAMOTO, AUTHOR 2 Y.MUTO,S.YOKOYAMA REVDAT 4 22-MAY-24 1FNX 1 REMARK REVDAT 3 23-FEB-22 1FNX 1 REMARK SEQADV REVDAT 2 24-FEB-09 1FNX 1 VERSN REVDAT 1 24-JUN-03 1FNX 0 JRNL AUTH M.INOUE,M.HIRAO,K.KASASHIMA,I.-S.KIM,G.KAWAI,T.KIGAWA, JRNL AUTH 2 H.SAKAMOTO,Y.MUTO,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF MOUSE HUC RNA-BINDING DOMAINS JRNL TITL 2 COMPLEXED WITH AN AU-RICH ELEMENT REVEALS DETERMINANTS OF JRNL TITL 3 NEURONAL DIFFERENTIATION JRNL REF TO BE PUBLISHED 2000 JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9, CNS 0.9 REMARK 3 AUTHORS : BRUNGER (CNS), BRUNGER ET AL. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FNX COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-AUG-00. REMARK 100 THE DEPOSITION ID IS D_1000011753. 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 : 20MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 20MM PHOSPHATE K BUFFER; 0.8MM REMARK 210 RBD1-RBD2 U-15N,13C; 0.8MM ARE; REMARK 210 1MM DTT; 100 UNITS/ML REMARK 210 RIBONUCLEASE INHIBITOR; 20MM REMARK 210 PHOSPHATE K BUFFER; 0.8MM RBD1- REMARK 210 RBD2; 0.8MM ARE U-15N,13C; 1MM REMARK 210 DTT; 100 UNITS/ML RIBONUCLEASE REMARK 210 INHIBITOR; 20MM PHOSPHATE K REMARK 210 BUFFER; 0.8MM RBD1-RBD2; 0.8MM REMARK 210 ARE U-15N,13C; 1MM DTT; 100 REMARK 210 UNITS/ML RIBONUCLEASE INHIBITOR; REMARK 210 20MM PHOSPHATE K BUFFER; 0.8MM REMARK 210 RBD1-RBD2; 0.8MM ARE U-15N,13C- REMARK 210 ADENOSINE; 1MM DTT; 100 UNITS/ML REMARK 210 RIBONUCLEASE INHIBITOR; 20MM REMARK 210 PHOSPHATE K BUFFER; 0.8MM RBD1- REMARK 210 RBD2; 0.8MM ARE U-15N,13C- REMARK 210 ADENOSINE; 1MM DTT; 100 UNITS/ML REMARK 210 RIBONUCLEASE INHIBITOR REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY. CONFORMER 21 IS THE REMARK 210 MINIMIZED AVERAGE STRUCTURE OF REMARK 210 CONFORMERS 1-20 REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 21 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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: R, H 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 O SER H 119 HZ2 LYS H 175 1.32 REMARK 500 O THR H 107 HZ3 LYS H 108 1.35 REMARK 500 OG1 THR H 153 HE ARG H 172 1.35 REMARK 500 OE2 GLU H 180 HZ3 LYS H 184 1.36 REMARK 500 HZ2 LYS H 139 OE1 GLU H 140 1.40 REMARK 500 O ASN H 101 HZ2 LYS H 111 1.44 REMARK 500 O ALA H 120 HZ3 LYS H 175 1.44 REMARK 500 OD1 ASN H 101 HZ3 LYS H 111 1.47 REMARK 500 HG1 THR H 39 OD1 ASN H 86 1.48 REMARK 500 OD2 ASP H 124 HH21 ARG H 176 1.48 REMARK 500 HO2' U R 4 O5' A R 5 1.49 REMARK 500 HH TYR H 128 OG SER H 130 1.49 REMARK 500 HO2' U R 6 O5' U R 7 1.49 REMARK 500 O GLU H 54 H LEU H 58 1.50 REMARK 500 HG SER H 130 OE2 GLU H 196 1.50 REMARK 500 O VAL H 129 H GLY H 169 1.51 REMARK 500 HG1 THR H 51 OD1 ASP H 53 1.52 REMARK 500 H VAL H 43 O GLY H 83 1.54 REMARK 500 O PRO H 47 H MET H 50 1.54 REMARK 500 O ALA H 179 H ILE H 183 1.54 REMARK 500 O ARG H 155 H PHE H 170 1.55 REMARK 500 O ARG H 176 H GLU H 180 1.55 REMARK 500 O GLU H 66 HG SER H 67 1.55 REMARK 500 H VAL H 129 O GLY H 169 1.56 REMARK 500 OE2 GLU H 54 HG SER H 57 1.56 REMARK 500 OH TYR H 45 HH12 ARG H 172 1.56 REMARK 500 O LYS H 139 H GLN H 143 1.56 REMARK 500 HG SER H 119 OD2 ASP H 174 1.58 REMARK 500 O LEU H 103 H ILE H 110 1.59 REMARK 500 O TYR H 128 H LYS H 201 1.59 REMARK 500 O GLU H 142 H SER H 146 1.59 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 12 TYR H 128 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 12 TYR H 128 CB - CG - CD1 ANGL. DEV. = 3.7 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 SER H 37 -38.78 163.48 REMARK 500 1 ASN H 40 64.03 -69.64 REMARK 500 1 GLN H 48 -39.19 -39.65 REMARK 500 1 ILE H 62 -49.31 -138.58 REMARK 500 1 ILE H 75 -54.31 -127.05 REMARK 500 1 SER H 79 120.47 85.04 REMARK 500 1 LEU H 80 -74.70 -79.75 REMARK 500 1 ASN H 101 49.29 -85.56 REMARK 500 1 SER H 118 122.82 176.84 REMARK 500 1 ALA H 120 80.45 64.29 REMARK 500 1 SER H 121 76.13 67.01 REMARK 500 1 ILE H 122 -86.44 -97.78 REMARK 500 1 ARG H 123 -152.93 56.87 REMARK 500 1 THR H 135 35.93 -89.21 REMARK 500 1 ARG H 150 102.13 -57.36 REMARK 500 1 LEU H 158 95.12 -160.72 REMARK 500 1 GLN H 160 29.65 -152.58 REMARK 500 1 ALA H 161 -46.26 -162.61 REMARK 500 1 ARG H 166 -73.96 -122.60 REMARK 500 1 ALA H 194 -172.63 -171.12 REMARK 500 1 ALA H 195 -70.37 -127.00 REMARK 500 1 ILE H 198 115.08 58.42 REMARK 500 1 ASN H 204 -79.38 -79.22 REMARK 500 1 ASN H 205 141.13 -177.51 REMARK 500 1 SER H 207 40.99 -140.70 REMARK 500 2 TYR H 45 47.96 71.43 REMARK 500 2 PRO H 47 98.25 -57.39 REMARK 500 2 ILE H 62 -50.68 -139.45 REMARK 500 2 SER H 67 156.64 177.17 REMARK 500 2 LYS H 74 31.87 -140.39 REMARK 500 2 ILE H 75 -51.35 -134.67 REMARK 500 2 GLN H 78 -84.66 -103.77 REMARK 500 2 SER H 79 124.02 71.84 REMARK 500 2 ASN H 101 39.84 -86.75 REMARK 500 2 THR H 107 -47.14 -178.06 REMARK 500 2 SER H 118 -88.01 -142.51 REMARK 500 2 SER H 119 -157.57 -135.09 REMARK 500 2 SER H 121 -76.91 -80.60 REMARK 500 2 ILE H 122 77.62 27.55 REMARK 500 2 ARG H 123 162.57 179.20 REMARK 500 2 THR H 135 47.72 -80.05 REMARK 500 2 LEU H 158 94.26 -160.61 REMARK 500 2 ALA H 161 -53.00 -138.41 REMARK 500 2 LEU H 186 -51.46 -122.40 REMARK 500 2 ALA H 194 -177.85 179.85 REMARK 500 2 ALA H 195 -75.56 -111.76 REMARK 500 2 ALA H 203 116.33 -37.01 REMARK 500 2 ASN H 204 74.92 -68.21 REMARK 500 2 SER H 207 -57.41 -143.16 REMARK 500 3 SER H 37 78.54 -173.94 REMARK 500 REMARK 500 THIS ENTRY HAS 488 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 7 U R 2 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1D8Z RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUC RBD1 REMARK 900 RELATED ID: 1D9A RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF HUC RBD2 DBREF 1FNX H 35 208 UNP Q60900 ELAV3_MOUSE 35 208 DBREF 1FNX R 0 9 PDB 1FNX 1FNX 0 9 SEQADV 1FNX MET H 35 UNP Q60900 ASP 35 CLONING ARTIFACT SEQRES 1 R 10 U A U U U A U U U U SEQRES 1 H 174 MET ASP SER LYS THR ASN LEU ILE VAL ASN TYR LEU PRO SEQRES 2 H 174 GLN ASN MET THR GLN ASP GLU PHE LYS SER LEU PHE GLY SEQRES 3 H 174 SER ILE GLY ASP ILE GLU SER CYS LYS LEU VAL ARG ASP SEQRES 4 H 174 LYS ILE THR GLY GLN SER LEU GLY TYR GLY PHE VAL ASN SEQRES 5 H 174 TYR SER ASP PRO ASN ASP ALA ASP LYS ALA ILE ASN THR SEQRES 6 H 174 LEU ASN GLY LEU LYS LEU GLN THR LYS THR ILE LYS VAL SEQRES 7 H 174 SER TYR ALA ARG PRO SER SER ALA SER ILE ARG ASP ALA SEQRES 8 H 174 ASN LEU TYR VAL SER GLY LEU PRO LYS THR MET SER GLN SEQRES 9 H 174 LYS GLU MET GLU GLN LEU PHE SER GLN TYR GLY ARG ILE SEQRES 10 H 174 ILE THR SER ARG ILE LEU LEU ASP GLN ALA THR GLY VAL SEQRES 11 H 174 SER ARG GLY VAL GLY PHE ILE ARG PHE ASP LYS ARG ILE SEQRES 12 H 174 GLU ALA GLU GLU ALA ILE LYS GLY LEU ASN GLY GLN LYS SEQRES 13 H 174 PRO LEU GLY ALA ALA GLU PRO ILE THR VAL LYS PHE ALA SEQRES 14 H 174 ASN ASN PRO SER GLN HELIX 1 1 THR H 51 SER H 61 1 11 HELIX 2 2 ASP H 89 LEU H 100 1 12 HELIX 3 3 SER H 137 GLN H 147 1 11 HELIX 4 4 LYS H 175 GLY H 185 1 11 SHEET 1 A 5 SER H 67 LEU H 70 0 SHEET 2 A 5 TYR H 82 ASN H 86 -1 N PHE H 84 O LYS H 69 SHEET 3 A 5 LEU H 41 ASN H 44 -1 O LEU H 41 N VAL H 85 SHEET 4 A 5 THR H 109 TYR H 114 -1 O LYS H 111 N ASN H 44 SHEET 5 A 5 ASN H 101 LYS H 104 -1 N GLY H 102 O ILE H 110 SHEET 1 B 4 ILE H 151 LEU H 157 0 SHEET 2 B 4 VAL H 168 PHE H 173 -1 O VAL H 168 N LEU H 157 SHEET 3 B 4 LEU H 127 SER H 130 -1 O LEU H 127 N ILE H 171 SHEET 4 B 4 THR H 199 PHE H 202 -1 O THR H 199 N SER H 130 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