HEADER RNA BINDING PROTEIN 22-FEB-25 9NGX TITLE STRUCTURE OF THE 5'SL-BOUND LA DOMAIN OF THE HUMAN LA-RELATED PROTEIN TITLE 2 6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LA-RELATED PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACHERON,ACHN,LA RIBONUCLEOPROTEIN DOMAIN FAMILY MEMBER 6; 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: LARP6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LA, LA-RELATED PROTEIN, LARP, LARP6, COLLAGEN SYNTHESIS, FIBROSIS, KEYWDS 2 RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.H.GORDON,R.SILVERS REVDAT 1 06-AUG-25 9NGX 0 JRNL AUTH B.H.GORDON,V.S.OGUNKUNLE,R.SILVERS JRNL TITL NONCANONICAL RNA BINDING OF HUMAN LA-RELATED PROTEIN 6. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 40705921 JRNL DOI 10.1093/NAR/GKAF682 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 3.98.15, AMBER 22 REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SIMULATED ANNEALING REMARK 4 REMARK 4 9NGX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000293352. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.7 MM [U-98% 13C; U-98% 15N] REMARK 210 LARP6(79-183), 1.7 MM A2M5, 10 REMARK 210 MM MES, 50 MM POTASSIUM CHLORIDE, REMARK 210 0.01 MG/ML DSS, 90% H2O/10% D2O; REMARK 210 370 UM [U-98% 13C; U-98% 15N] REMARK 210 LARP6(79-183), 370 UM A2M5, 10 REMARK 210 MM MES, 50 MM POTASSIUM CHLORIDE, REMARK 210 0.01 MG/ML DSS, 100% D2O; 300 REMARK 210 UM [U-98% 15N] LARP6(79-183), REMARK 210 300 UM A2M5, 10 MM MES, 50 MM REMARK 210 POTASSIUM CHLORIDE, 0.01 MG/ML REMARK 210 DSS, 90% H2O/10% D2O; 1.1 MM [U- REMARK 210 98% 13C; U-98% 15N] LARP6(79-183) REMARK 210 , 1.1 MM A2M5, 10 MM MES, 50 MM REMARK 210 POTASSIUM CHLORIDE, 0.01 MG/ML REMARK 210 DSS, 90% H2O/10% D2O; 1.6 MM [U- REMARK 210 98% 15N; 1,3-13C-GLYCEROL] REMARK 210 LARP6(79-183), 1.6 MM A2M5, 10 REMARK 210 MM MES, 50 MM POTASSIUM CHLORIDE, REMARK 210 0.01 MG/ML DSS, 100% D2O; 1.3 REMARK 210 MM [U-98% 15N; 2-13C-GLYCEROL] REMARK 210 LARP6(79-183), 1.3 MM A2M5, 10 REMARK 210 MM MES, 50 MM POTASSIUM CHLORIDE, REMARK 210 0.01 MG/ML DSS, 100% D2O; 1.9 REMARK 210 MM [13C, 15N]-ARG LARP6(79-183), REMARK 210 1.9 MM A2M5, 10 MM MES, 50 MM REMARK 210 POTASSIUM CHLORIDE, 0.01 MG/ML REMARK 210 DSS, 90% H2O/10% D2O; 1 MM [13C]- REMARK 210 PRO LARP6(79-183), 1 MM A2M5, 10 REMARK 210 MM MES, 50 MM POTASSIUM CHLORIDE, REMARK 210 0.01 MG/ML DSS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 H(CC)(CO)NH; 3D (H)CC(CO)NH; 3D REMARK 210 HCCH-COSY; 2D 1H-13C HSQC; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-13C CTHSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.6.5, TOPSPIN 4.3.0, REMARK 210 NMRFAM-SPARKY, ARTINA, TALOS-N REMARK 210 4.12 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 168 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 4 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 6 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 7 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 9 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 10 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 18 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 20 ARG A 168 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ASP A 112 78.98 -109.08 REMARK 500 2 ASP A 112 75.84 -114.92 REMARK 500 2 ASN A 180 55.12 -99.95 REMARK 500 3 ASP A 112 76.91 -101.50 REMARK 500 5 LEU A 81 137.68 81.28 REMARK 500 5 ASP A 112 78.70 -107.76 REMARK 500 6 LEU A 81 71.97 -108.84 REMARK 500 6 GLN A 83 30.52 -79.50 REMARK 500 6 ASP A 112 78.37 -104.03 REMARK 500 7 ASP A 112 76.23 -102.55 REMARK 500 8 ASP A 112 74.74 -105.85 REMARK 500 9 ASP A 80 49.49 -91.24 REMARK 500 9 GLN A 83 31.14 -87.58 REMARK 500 10 ASP A 80 -60.26 -124.25 REMARK 500 10 LEU A 81 -154.88 -128.71 REMARK 500 11 ASP A 112 79.36 -105.78 REMARK 500 12 LEU A 81 75.09 -102.50 REMARK 500 12 ASP A 112 78.40 -101.35 REMARK 500 14 ASP A 112 78.22 -102.43 REMARK 500 15 LEU A 181 144.90 80.90 REMARK 500 16 GLU A 84 146.54 66.25 REMARK 500 17 GLN A 83 34.41 -89.12 REMARK 500 17 ASP A 112 78.41 -100.99 REMARK 500 18 GLN A 83 40.08 -82.90 REMARK 500 18 ASP A 112 79.18 -100.38 REMARK 500 19 GLN A 83 32.51 -86.56 REMARK 500 19 ASP A 112 75.51 -102.85 REMARK 500 20 GLU A 82 28.92 -142.42 REMARK 500 20 ASP A 112 77.93 -108.91 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 9 ARG A 120 0.09 SIDE CHAIN REMARK 500 10 ARG A 146 0.08 SIDE CHAIN REMARK 500 14 ARG A 120 0.08 SIDE CHAIN REMARK 500 16 ARG A 120 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 31231 RELATED DB: BMRB REMARK 900 STRUCTURE OF THE 5'SL-BOUND LA MOTIF OF THE HUMAN LA-RELATED REMARK 900 PROTEIN 6 DBREF 9NGX A 79 183 UNP Q9BRS8 LARP6_HUMAN 79 183 SEQADV 9NGX GLY A 78 UNP Q9BRS8 EXPRESSION TAG SEQRES 1 A 106 GLY GLU ASP LEU GLU GLN GLU TRP LYS PRO PRO ASP GLU SEQRES 2 A 106 GLU LEU ILE LYS LYS LEU VAL ASP GLN ILE GLU PHE TYR SEQRES 3 A 106 PHE SER ASP GLU ASN LEU GLU LYS ASP ALA PHE LEU LEU SEQRES 4 A 106 LYS HIS VAL ARG ARG ASN LYS LEU GLY TYR VAL SER VAL SEQRES 5 A 106 LYS LEU LEU THR SER PHE LYS LYS VAL LYS HIS LEU THR SEQRES 6 A 106 ARG ASP TRP ARG THR THR ALA HIS ALA LEU LYS TYR SER SEQRES 7 A 106 VAL VAL LEU GLU LEU ASN GLU ASP HIS ARG LYS VAL ARG SEQRES 8 A 106 ARG THR THR PRO VAL PRO LEU PHE PRO ASN GLU ASN LEU SEQRES 9 A 106 PRO SER HELIX 1 AA1 GLU A 90 PHE A 104 1 15 HELIX 2 AA2 ASP A 106 LYS A 111 1 6 HELIX 3 AA3 ALA A 113 ARG A 121 1 9 HELIX 4 AA4 VAL A 129 SER A 134 1 6 HELIX 5 AA5 LYS A 137 LEU A 141 1 5 HELIX 6 AA6 TRP A 145 TYR A 154 1 10 HELIX 7 AA7 PRO A 177 ASN A 180 5 4 SHEET 1 AA1 3 TYR A 126 SER A 128 0 SHEET 2 AA1 3 LYS A 166 ARG A 169 -1 O VAL A 167 N VAL A 127 SHEET 3 AA1 3 LEU A 158 LEU A 160 -1 N GLU A 159 O ARG A 168 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 228 0 0 7 3 0 0 6 894 1 0 9 END