HEADER RNA BINDING PROTEIN 22-NOV-18 6I9B TITLE NMR STRUCTURE OF THE LA MODULE FROM HUMAN LARP4A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LA-RELATED PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LA RIBONUCLEOPROTEIN DOMAIN FAMILY MEMBER 4; COMPND 5 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: LARP4, PP13296; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA II KEYWDS LA-RELATED PROTEINS, LARPS, PABP-BINDING PROTEIN, LA MODULE, RNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.R.CONTE,L.MARTINO,R.A.ATKINSON,G.KELLY,I.CRUZ-GALLARDO,S.DE TITO, AUTHOR 2 R.TROTTA REVDAT 6 19-JUN-24 6I9B 1 REMARK REVDAT 5 14-JUN-23 6I9B 1 REMARK REVDAT 4 13-JUL-22 6I9B 1 AUTHOR REMARK REVDAT 3 03-JUL-19 6I9B 1 JRNL REVDAT 2 08-MAY-19 6I9B 1 REMARK REVDAT 1 13-MAR-19 6I9B 0 JRNL AUTH I.CRUZ-GALLARDO,L.MARTINO,G.KELLY,R.A.ATKINSON,R.TROTTA, JRNL AUTH 2 S.DE TITO,P.COLEMAN,Z.AHDASH,Y.GU,T.T.T.BUI,M.R.CONTE JRNL TITL LARP4A RECOGNIZES POLYA RNA VIA A NOVEL BINDING MECHANISM JRNL TITL 2 MEDIATED BY DISORDERED REGIONS AND INVOLVING THE PAM2W JRNL TITL 3 MOTIF, REVEALING INTERPLAY BETWEEN PABP, LARP4A AND MRNA. JRNL REF NUCLEIC ACIDS RES. V. 47 4272 2019 JRNL REFN ESSN 1362-4962 JRNL PMID 30820564 JRNL DOI 10.1093/NAR/GKZ144 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XPLOR-NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6I9B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1200012913. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.25 REMARK 210 IONIC STRENGTH : 100 MM KCL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM [U-99% 15N] RNA BINDING REMARK 210 PROTEIN, 90% H2O/10% D2O; 400 UM REMARK 210 [U-99% 13C; U-99% 15N] RNA REMARK 210 BINDING PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 2D 1H-15N HSQC; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D 1H- REMARK 210 13C NOESY AROMATIC; 3D HCCH- REMARK 210 TOCSY; 3D HNCA; 3D HN(CO)CA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, XEASY, CCPNMR REMARK 210 ANALYSIS, CANDID, TALOS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 H ASP A 147 O PHE A 151 1.26 REMARK 500 H1 ASN A 111 H SER A 112 1.33 REMARK 500 H ILE A 152 O VAL A 192 1.54 REMARK 500 O MET A 160 H LYS A 164 1.58 REMARK 500 O LEU A 136 H ASP A 139 1.58 REMARK 500 O VAL A 157 H MET A 160 1.59 REMARK 500 N ASP A 147 O PHE A 151 2.15 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 ALA A 113 -158.32 -133.77 REMARK 500 1 ASP A 139 77.06 -117.21 REMARK 500 1 MET A 146 122.57 -32.33 REMARK 500 1 ASP A 147 -144.29 -65.08 REMARK 500 1 ALA A 158 -11.66 -45.73 REMARK 500 1 THR A 167 -172.98 177.06 REMARK 500 1 GLU A 190 -13.29 -140.27 REMARK 500 1 VAL A 192 139.91 -175.08 REMARK 500 1 LYS A 197 -107.17 -103.22 REMARK 500 1 ARG A 198 87.61 55.76 REMARK 500 1 LYS A 220 125.62 -32.01 REMARK 500 1 HIS A 234 166.42 -38.62 REMARK 500 1 ASN A 235 37.42 72.46 REMARK 500 1 SER A 236 14.37 42.74 REMARK 500 1 ASN A 275 -158.64 -158.11 REMARK 500 2 ALA A 113 117.09 58.17 REMARK 500 2 VAL A 114 89.19 50.15 REMARK 500 2 ASP A 139 75.02 -110.56 REMARK 500 2 MET A 146 118.10 -31.24 REMARK 500 2 ASP A 147 -144.38 -66.01 REMARK 500 2 ALA A 158 -16.49 -45.53 REMARK 500 2 THR A 167 -168.39 165.51 REMARK 500 2 SER A 179 15.79 -68.24 REMARK 500 2 VAL A 192 140.04 -174.59 REMARK 500 2 HIS A 196 -10.74 -142.64 REMARK 500 2 LYS A 197 68.09 -113.41 REMARK 500 2 LYS A 220 119.69 -32.76 REMARK 500 2 ASN A 235 19.78 50.35 REMARK 500 2 SER A 236 -40.81 -171.36 REMARK 500 2 ASN A 275 97.48 71.44 REMARK 500 2 LYS A 280 94.80 -67.45 REMARK 500 2 ARG A 284 -109.72 -81.56 REMARK 500 3 SER A 112 46.76 -75.14 REMARK 500 3 ASP A 139 67.59 -105.35 REMARK 500 3 MET A 146 122.71 -31.30 REMARK 500 3 ASP A 147 -144.05 -64.90 REMARK 500 3 THR A 167 178.82 175.36 REMARK 500 3 VAL A 192 139.98 -174.46 REMARK 500 3 HIS A 196 -147.76 -75.45 REMARK 500 3 VAL A 227 134.64 -34.88 REMARK 500 3 ASN A 235 19.89 41.45 REMARK 500 3 SER A 236 -44.20 -168.28 REMARK 500 3 THR A 276 21.15 -77.82 REMARK 500 3 ALA A 279 99.77 -178.37 REMARK 500 4 ALA A 113 -147.75 -61.98 REMARK 500 4 VAL A 114 -82.64 -95.78 REMARK 500 4 ASP A 139 78.28 -109.36 REMARK 500 4 MET A 146 120.44 -34.64 REMARK 500 4 ASP A 147 -144.15 -64.85 REMARK 500 4 ALA A 158 -13.53 -47.67 REMARK 500 REMARK 500 THIS ENTRY HAS 326 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27666 RELATED DB: BMRB DBREF 6I9B A 111 287 UNP Q71RC2 LARP4_HUMAN 111 287 SEQRES 1 A 177 ASN SER ALA VAL SER THR GLU ASP LEU LYS GLU CYS LEU SEQRES 2 A 177 LYS LYS GLN LEU GLU PHE CYS PHE SER ARG GLU ASN LEU SEQRES 3 A 177 SER LYS ASP LEU TYR LEU ILE SER GLN MET ASP SER ASP SEQRES 4 A 177 GLN PHE ILE PRO ILE TRP THR VAL ALA ASN MET GLU GLU SEQRES 5 A 177 ILE LYS LYS LEU THR THR ASP PRO ASP LEU ILE LEU GLU SEQRES 6 A 177 VAL LEU ARG SER SER PRO MET VAL GLN VAL ASP GLU LYS SEQRES 7 A 177 GLY GLU LYS VAL ARG PRO SER HIS LYS ARG CYS ILE VAL SEQRES 8 A 177 ILE LEU ARG GLU ILE PRO GLU THR THR PRO ILE GLU GLU SEQRES 9 A 177 VAL LYS GLY LEU PHE LYS SER GLU ASN CYS PRO LYS VAL SEQRES 10 A 177 ILE SER CYS GLU PHE ALA HIS ASN SER ASN TRP TYR ILE SEQRES 11 A 177 THR PHE GLN SER ASP THR ASP ALA GLN GLN ALA PHE LYS SEQRES 12 A 177 TYR LEU ARG GLU GLU VAL LYS THR PHE GLN GLY LYS PRO SEQRES 13 A 177 ILE MET ALA ARG ILE LYS ALA ILE ASN THR PHE PHE ALA SEQRES 14 A 177 LYS ASN GLY TYR ARG LEU MET ASP HELIX 1 AA1 THR A 116 PHE A 131 1 16 HELIX 2 AA2 SER A 132 SER A 137 1 6 HELIX 3 AA3 TYR A 141 MET A 146 1 6 HELIX 4 AA4 PRO A 153 ASN A 159 1 7 HELIX 5 AA5 MET A 160 LYS A 165 1 6 HELIX 6 AA6 ASP A 169 ARG A 178 1 10 HELIX 7 AA7 PRO A 211 LYS A 220 1 10 HELIX 8 AA8 SER A 244 VAL A 259 1 16 SHEET 1 AA1 2 VAL A 183 VAL A 185 0 SHEET 2 AA1 2 VAL A 192 PRO A 194 -1 O ARG A 193 N GLN A 184 SHEET 1 AA2 4 SER A 229 ALA A 233 0 SHEET 2 AA2 4 ASN A 237 THR A 241 -1 O THR A 241 N SER A 229 SHEET 3 AA2 4 ILE A 200 LEU A 203 -1 N VAL A 201 O ILE A 240 SHEET 4 AA2 4 ALA A 269 LYS A 272 -1 O LYS A 272 N ILE A 200 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