HEADER RNA BINDING PROTEIN 11-MAR-13 2M5W TITLE NMR SOLUTION STRUCTURE OF THE LA MOTIF (N-TERMINAL DOMAIN, NTD) OF TITLE 2 DICTYOSTELIUM DISCOIDEUM LA PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LUPUS LA PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LA-TYPE RNA-BINDING DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DICTYOSTELIUM DISCOIDEUM; SOURCE 3 ORGANISM_COMMON: SLIME MOLD; SOURCE 4 ORGANISM_TAXID: 44689; SOURCE 5 GENE: DDB_0204655, DDB_G0281763; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS LUPUS PROTEIN, LA MOTIF, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 31 MDLTYP MINIMIZED AVERAGE AUTHOR D.J.VOURTSIS,C.T.CHASAPIS,M.APOSTOLIDI,C.STATHOPOULOS,D.BENTROP, AUTHOR 2 G.A.SPYROULIAS REVDAT 2 14-JUN-23 2M5W 1 REMARK REVDAT 1 12-MAR-14 2M5W 0 JRNL AUTH D.J.VOURTSIS,C.T.CHASAPIS,M.APOSTOLIDI,C.STATHOPOULOS, JRNL AUTH 2 D.BENTROP,G.A.SPYROULIAS JRNL TITL NMR SOLUTION STRUCTURE OF THE LA MOTIF (N-TERMINAL DOMAIN, JRNL TITL 2 NTD) OF DICTYOSTELIUM DISCOIDEUM LA PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.APOSTOLIDI,D.J.VOURTSIS,C.T.CHASAPIS,C.STATHOPOULOS, REMARK 1 AUTH 2 D.BENTROP,G.A.SPYROULIAS REMARK 1 TITL (1)H, (15)N, (13)C ASSIGNMENT AND SECONDARY STRUCTURE REMARK 1 TITL 2 DETERMINATION OF TWO DOMAINS OF LA PROTEIN FROM D. REMARK 1 TITL 3 DISCOIDEUM. REMARK 1 REF BIOMOL.NMR ASSIGN. REMARK 1 REFN ESSN 1874-270X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CARA 1.8.4, AMBER_5.0 REMARK 3 AUTHORS : KELLER AND WUTHRICH (CARA), CASE, D.A. ET AL. REMARK 3 (AMBER_5.0) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000103248. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.37 MM [U-98% 15N] LA-TYPE RNA REMARK 210 -BINDING DOMAIN, 50 MM BUFFER REMARK 210 SALTS, 90% H2O/10% D2O; 0.37 MM REMARK 210 [U-98% 13C; U-98% 15N] LA-TYPE REMARK 210 RNA-BINDING DOMAIN, 50 MM BUFFER REMARK 210 SALTS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HN(CO)CA; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 400 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DPX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS, RESTRAINED REMARK 210 ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 31 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 31 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 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 24 ARG A 82 NE - CZ - NH2 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 SER A 2 -150.38 51.24 REMARK 500 1 SER A 20 32.10 35.36 REMARK 500 1 ASN A 35 61.33 -157.86 REMARK 500 1 VAL A 36 -74.29 66.34 REMARK 500 1 ASP A 37 34.38 -160.78 REMARK 500 1 PHE A 48 7.43 -68.85 REMARK 500 1 ASN A 49 -77.12 61.47 REMARK 500 1 THR A 56 -19.88 63.09 REMARK 500 2 ASN A 35 59.29 -155.31 REMARK 500 2 VAL A 36 -76.62 64.47 REMARK 500 2 ASP A 37 35.96 -163.96 REMARK 500 2 ASN A 49 -76.95 58.12 REMARK 500 2 THR A 56 -9.04 62.38 REMARK 500 2 LYS A 67 31.58 -97.10 REMARK 500 3 SER A 2 -167.06 -77.30 REMARK 500 3 SER A 20 35.36 38.93 REMARK 500 3 ASN A 35 64.08 -158.17 REMARK 500 3 VAL A 36 -76.03 63.59 REMARK 500 3 ASP A 37 32.92 -163.47 REMARK 500 3 ASN A 49 -71.80 68.58 REMARK 500 3 THR A 69 -65.87 -123.49 REMARK 500 4 ALA A 33 2.84 -66.34 REMARK 500 4 ASN A 35 64.33 -150.95 REMARK 500 4 VAL A 36 -77.29 63.88 REMARK 500 4 ASP A 37 33.24 -163.36 REMARK 500 4 ASN A 49 -69.64 71.23 REMARK 500 4 THR A 56 -11.00 62.74 REMARK 500 4 THR A 69 -74.21 -105.85 REMARK 500 4 ARG A 82 -176.12 -66.80 REMARK 500 5 SER A 2 -175.37 -170.09 REMARK 500 5 ASN A 35 65.96 -155.95 REMARK 500 5 VAL A 36 -75.16 64.64 REMARK 500 5 ASP A 37 28.96 -161.03 REMARK 500 5 ASN A 49 -74.21 69.34 REMARK 500 5 THR A 56 -4.60 60.42 REMARK 500 5 LYS A 67 44.99 -108.94 REMARK 500 6 ALA A 33 15.19 -68.50 REMARK 500 6 ASN A 35 64.63 -151.41 REMARK 500 6 VAL A 36 -76.92 64.66 REMARK 500 6 ASP A 37 30.66 -162.43 REMARK 500 6 PHE A 48 9.35 -69.91 REMARK 500 6 ASN A 49 -75.73 60.89 REMARK 500 6 THR A 56 -18.65 66.07 REMARK 500 7 SER A 20 26.19 49.05 REMARK 500 7 ASN A 35 55.83 -146.68 REMARK 500 7 VAL A 36 -76.12 66.85 REMARK 500 7 ASP A 37 36.88 -162.30 REMARK 500 7 ASN A 49 -69.68 63.86 REMARK 500 7 THR A 56 -7.13 62.25 REMARK 500 7 SER A 74 -154.64 -165.18 REMARK 500 REMARK 500 THIS ENTRY HAS 246 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 TYR A 15 0.08 SIDE CHAIN REMARK 500 1 TYR A 16 0.07 SIDE CHAIN REMARK 500 2 TYR A 15 0.08 SIDE CHAIN REMARK 500 2 TYR A 16 0.08 SIDE CHAIN REMARK 500 2 ARG A 50 0.08 SIDE CHAIN REMARK 500 2 ARG A 82 0.14 SIDE CHAIN REMARK 500 3 TYR A 15 0.09 SIDE CHAIN REMARK 500 4 TYR A 15 0.08 SIDE CHAIN REMARK 500 4 ARG A 50 0.09 SIDE CHAIN REMARK 500 5 TYR A 15 0.07 SIDE CHAIN REMARK 500 6 TYR A 15 0.08 SIDE CHAIN REMARK 500 6 TYR A 16 0.08 SIDE CHAIN REMARK 500 8 TYR A 15 0.07 SIDE CHAIN REMARK 500 8 TYR A 16 0.07 SIDE CHAIN REMARK 500 8 ARG A 82 0.10 SIDE CHAIN REMARK 500 9 TYR A 15 0.07 SIDE CHAIN REMARK 500 9 PHE A 48 0.08 SIDE CHAIN REMARK 500 10 TYR A 15 0.10 SIDE CHAIN REMARK 500 11 TYR A 15 0.07 SIDE CHAIN REMARK 500 11 TYR A 16 0.07 SIDE CHAIN REMARK 500 12 TYR A 15 0.08 SIDE CHAIN REMARK 500 12 TYR A 16 0.10 SIDE CHAIN REMARK 500 13 TYR A 16 0.08 SIDE CHAIN REMARK 500 14 TYR A 15 0.09 SIDE CHAIN REMARK 500 16 TYR A 15 0.10 SIDE CHAIN REMARK 500 16 TYR A 16 0.08 SIDE CHAIN REMARK 500 17 TYR A 15 0.07 SIDE CHAIN REMARK 500 17 TYR A 16 0.07 SIDE CHAIN REMARK 500 19 TYR A 15 0.08 SIDE CHAIN REMARK 500 19 TYR A 16 0.08 SIDE CHAIN REMARK 500 20 TYR A 15 0.09 SIDE CHAIN REMARK 500 21 TYR A 15 0.08 SIDE CHAIN REMARK 500 21 TYR A 16 0.08 SIDE CHAIN REMARK 500 22 TYR A 15 0.09 SIDE CHAIN REMARK 500 23 TYR A 15 0.09 SIDE CHAIN REMARK 500 23 ARG A 70 0.11 SIDE CHAIN REMARK 500 24 TYR A 15 0.07 SIDE CHAIN REMARK 500 25 TYR A 16 0.08 SIDE CHAIN REMARK 500 26 ARG A 82 0.18 SIDE CHAIN REMARK 500 27 TYR A 15 0.09 SIDE CHAIN REMARK 500 29 ARG A 82 0.09 SIDE CHAIN REMARK 500 30 TYR A 15 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S7A RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE LA MOTIF OF HUMAN LA PROTEIN REMARK 900 RELATED ID: 1S29 RELATED DB: PDB REMARK 900 LA AUTOANTIGEN N-TERMINAL DOMAIN REMARK 900 RELATED ID: 2VON RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N-TERMINAL DOMAINS OF HUMAN LA PROTEIN REMARK 900 COMPLEXED WITH RNA OLIGOMER AUAAUUU REMARK 900 RELATED ID: 18620 RELATED DB: BMRB REMARK 900 RRM DOMAIN REMARK 900 RELATED ID: 18621 RELATED DB: BMRB DBREF 2M5W A 1 91 UNP Q54TG6 Q54TG6_DICDI 1 91 SEQRES 1 A 91 MET SER GLU GLU THR SER THR GLN ILE LEU LYS GLN VAL SEQRES 2 A 91 GLU TYR TYR PHE SER ASP SER ASN PHE PRO ARG ASP LYS SEQRES 3 A 91 PHE LEU ARG SER GLU ALA ALA LYS ASN VAL ASP ASN TYR SEQRES 4 A 91 ILE SER ILE ASP VAL ILE ALA SER PHE ASN ARG MET LYS SEQRES 5 A 91 THR ILE SER THR ASP LEU GLN LEU ILE THR GLU ALA LEU SEQRES 6 A 91 LYS LYS SER THR ARG LEU GLN VAL SER GLU ASP GLY LYS SEQRES 7 A 91 MET VAL ARG ARG LEU ASP PRO LEU PRO GLU ASN ILE ASP HELIX 1 1 MET A 1 ASP A 19 1 19 HELIX 2 2 ASP A 25 ALA A 33 1 9 HELIX 3 3 SER A 41 SER A 47 1 7 HELIX 4 4 ASN A 49 THR A 56 1 8 HELIX 5 5 ASP A 57 LYS A 67 1 11 SHEET 1 A 2 LEU A 71 VAL A 73 0 SHEET 2 A 2 VAL A 80 ARG A 82 -1 O ARG A 81 N GLN A 72 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