HEADER TRANSLATION/RNA 21-MAY-07 2JPP TITLE STRUCTURAL BASIS OF RSMA/CSRA RNA RECOGNITION: STRUCTURE OF RSME BOUND TITLE 2 TO THE SHINE-DALGARNO SEQUENCE OF HCNA MRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*GP*GP*CP*UP*UP*CP*AP*CP*GP*GP*AP*UP*GP*AP*AP*GP*CP*CP*C)-3'); COMPND 4 CHAIN: C, D; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TRANSLATIONAL REPRESSOR; COMPND 8 CHAIN: A, B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: PSEUDOMONAS FLUORESCENS; SOURCE 5 ORGANISM_TAXID: 294; SOURCE 6 GENE: RSME; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+RIL; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS RNA RECOGNITION, PROTEIN/RNA, CSRA, RSMA, SHINE-DALGARNO, KEYWDS 2 TRANSLATION-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.SCHUBERT,K.LAPOUGE,O.DUSS,F.C.OBERSTRASS,I.JELESAROV,D.HAAS,F.H.- AUTHOR 2 T.ALLAIN REVDAT 4 09-MAR-22 2JPP 1 REMARK SEQADV ATOM REVDAT 3 24-FEB-09 2JPP 1 VERSN REVDAT 2 18-SEP-07 2JPP 1 JRNL REVDAT 1 21-AUG-07 2JPP 0 JRNL AUTH M.SCHUBERT,K.LAPOUGE,O.DUSS,F.C.OBERSTRASS,I.JELESAROV, JRNL AUTH 2 D.HAAS,F.H.-T.ALLAIN JRNL TITL MOLECULAR BASIS OF MESSENGER RNA RECOGNITION BY THE SPECIFIC JRNL TITL 2 BACTERIAL REPRESSING CLAMP RSMA/CSRA JRNL REF NAT.STRUCT.MOL.BIOL. V. 14 807 2007 JRNL REFN ISSN 1545-9993 JRNL PMID 17704818 JRNL DOI 10.1038/NSMB1285 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN IMPLICIT WATER REMARK 4 REMARK 4 2JPP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100133. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.18 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] RSME, 1 MM REMARK 210 RNA, 93% H2O/7% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N] RSME, 1 MM RNA, REMARK 210 100% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N] RSME, 1 MM RNA, 93% REMARK 210 H2O/7% D2O; 1 MM [U-100% 15N] REMARK 210 RSME, 1 MM RNA, 100% D2O; 1 MM REMARK 210 [U-100% 15N] RSME, 1 MM [U-13C; REMARK 210 U-15N]-GUA/URA RNA, 93% H2O/7% REMARK 210 D2O; 1 MM [U-100% 15N] RSME, 1 REMARK 210 MM [U-13C; U-15N]-GUA/URA RNA, REMARK 210 100% D2O; 1 MM [U-100% 15N] RSME, REMARK 210 1 MM [U-13C; U-15N]-CYT/ADE RNA, REMARK 210 100% D2O; 1 MM [U-100% 15N] REMARK 210 RSME, 1 MM [U-13C; U-15N]-CYT/ REMARK 210 ADE RNA, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCA; 3D REMARK 210 HNCACB; 3D HNCO; 2D 1H-1H TOCSY; REMARK 210 3D H(CCO)NH; 2D 1H-1H NOESY; 2D REMARK 210 1H-13C HSQC; 3D 1H-13C NOESY; 3D REMARK 210 HN(CO)CA; 2D 1FF2FF NOESY; 3D REMARK 210 1FE3FF NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : DMX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 3.02, SPARKY, CCP4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A 54 REMARK 465 LEU A 55 REMARK 465 THR A 56 REMARK 465 ALA A 57 REMARK 465 PRO A 58 REMARK 465 ASP A 59 REMARK 465 LYS A 60 REMARK 465 ARG A 61 REMARK 465 GLU A 62 REMARK 465 THR A 63 REMARK 465 PRO A 64 REMARK 465 HIS A 65 REMARK 465 HIS A 66 REMARK 465 HIS A 67 REMARK 465 HIS A 68 REMARK 465 HIS A 69 REMARK 465 HIS A 70 REMARK 465 GLY B 54 REMARK 465 LEU B 55 REMARK 465 THR B 56 REMARK 465 ALA B 57 REMARK 465 PRO B 58 REMARK 465 ASP B 59 REMARK 465 LYS B 60 REMARK 465 ARG B 61 REMARK 465 GLU B 62 REMARK 465 THR B 63 REMARK 465 PRO B 64 REMARK 465 HIS B 65 REMARK 465 HIS B 66 REMARK 465 HIS B 67 REMARK 465 HIS B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 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 G C 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 G D 11 O4' - C1' - N9 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 G C 11 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 C D 9 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 2 G D 11 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 3 G C 11 O4' - C1' - N9 ANGL. DEV. = 6.9 DEGREES REMARK 500 3 A C 12 C5' - C4' - C3' ANGL. DEV. = -8.4 DEGREES REMARK 500 3 G D 11 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 4 G C 11 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 4 G D 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 C C 9 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 G C 11 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 5 G D 11 O4' - C1' - N9 ANGL. DEV. = 6.2 DEGREES REMARK 500 5 A D 12 C5' - C4' - C3' ANGL. DEV. = -8.6 DEGREES REMARK 500 6 G C 11 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 6 A C 12 C5' - C4' - C3' ANGL. DEV. = -8.8 DEGREES REMARK 500 7 G C 11 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 G D 11 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 7 A D 12 C5' - C4' - C3' ANGL. DEV. = -8.7 DEGREES REMARK 500 8 G C 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 C D 9 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 G D 11 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 G C 11 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 10 G C 11 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 10 G D 11 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 A D 12 C5' - C4' - C3' ANGL. DEV. = -9.6 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 B 26 44.83 -151.99 REMARK 500 2 SER A 26 41.43 -149.12 REMARK 500 2 SER B 26 38.95 -146.91 REMARK 500 3 THR A 5 79.05 -118.32 REMARK 500 3 GLU A 46 0.91 -68.88 REMARK 500 3 SER B 26 40.45 -145.75 REMARK 500 3 GLU B 45 -83.30 39.89 REMARK 500 4 SER B 26 35.28 -149.58 REMARK 500 4 ILE B 47 -33.83 -133.41 REMARK 500 5 SER A 26 33.85 -146.93 REMARK 500 5 ILE A 51 -53.58 -128.50 REMARK 500 5 SER B 26 46.80 -141.08 REMARK 500 5 GLU B 45 -56.34 70.54 REMARK 500 5 GLU B 46 0.49 -66.52 REMARK 500 6 GLU A 45 -89.87 41.46 REMARK 500 6 SER B 26 39.37 -146.96 REMARK 500 7 SER B 26 44.17 -150.13 REMARK 500 7 GLN B 52 -5.20 -56.29 REMARK 500 8 SER A 26 39.53 -150.26 REMARK 500 9 SER A 26 39.92 -149.11 REMARK 500 9 ILE A 51 -89.16 -103.51 REMARK 500 10 ASP A 16 18.10 57.81 REMARK 500 10 SER A 26 45.42 -151.69 REMARK 500 10 ILE A 51 -91.44 -112.73 REMARK 500 10 GLU B 45 -98.68 41.95 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 4 A C 12 0.06 SIDE CHAIN REMARK 500 5 C C 9 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2JPP A 1 64 UNP Q5MXB2 Q5MXB2_PSEFL 1 64 DBREF 2JPP B 1 64 UNP Q5MXB2 Q5MXB2_PSEFL 1 64 DBREF 2JPP C 1 20 PDB 2JPP 2JPP 1 20 DBREF 2JPP D 1 20 PDB 2JPP 2JPP 1 20 SEQADV 2JPP HIS A 65 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS A 66 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS A 67 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS A 68 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS A 69 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS A 70 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS B 65 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS B 66 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS B 67 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS B 68 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS B 69 UNP Q5MXB2 EXPRESSION TAG SEQADV 2JPP HIS B 70 UNP Q5MXB2 EXPRESSION TAG SEQRES 1 C 20 G G G C U U C A C G G A U SEQRES 2 C 20 G A A G C C C SEQRES 1 D 20 G G G C U U C A C G G A U SEQRES 2 D 20 G A A G C C C SEQRES 1 A 70 MET LEU ILE LEU THR ARG LYS VAL GLY GLU SER ILE ASN SEQRES 2 A 70 ILE GLY ASP ASP ILE THR ILE THR ILE LEU GLY VAL SER SEQRES 3 A 70 GLY GLN GLN VAL ARG ILE GLY ILE ASN ALA PRO LYS ASP SEQRES 4 A 70 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 A 70 ALA GLY LEU THR ALA PRO ASP LYS ARG GLU THR PRO HIS SEQRES 6 A 70 HIS HIS HIS HIS HIS SEQRES 1 B 70 MET LEU ILE LEU THR ARG LYS VAL GLY GLU SER ILE ASN SEQRES 2 B 70 ILE GLY ASP ASP ILE THR ILE THR ILE LEU GLY VAL SER SEQRES 3 B 70 GLY GLN GLN VAL ARG ILE GLY ILE ASN ALA PRO LYS ASP SEQRES 4 B 70 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 B 70 ALA GLY LEU THR ALA PRO ASP LYS ARG GLU THR PRO HIS SEQRES 6 B 70 HIS HIS HIS HIS HIS HELIX 1 1 GLU A 45 GLN A 52 1 8 HELIX 2 2 GLU B 45 GLN B 49 1 5 SHEET 1 A 5 LEU A 2 LYS A 7 0 SHEET 2 A 5 GLN B 29 ASN B 35 -1 O ILE B 34 N LEU A 2 SHEET 3 A 5 ILE B 18 SER B 26 -1 N THR B 19 O ASN B 35 SHEET 4 A 5 SER B 11 ILE B 14 -1 N ILE B 12 O ILE B 20 SHEET 5 A 5 VAL A 42 ARG A 44 -1 N HIS A 43 O ASN B 13 SHEET 1 B 5 LEU B 2 LYS B 7 0 SHEET 2 B 5 GLN A 29 ASN A 35 -1 N ILE A 34 O LEU B 2 SHEET 3 B 5 ILE A 18 SER A 26 -1 N THR A 19 O ASN A 35 SHEET 4 B 5 SER A 11 ILE A 14 -1 N ILE A 14 O ILE A 18 SHEET 5 B 5 VAL B 42 ARG B 44 -1 O HIS B 43 N ASN A 13 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10