HEADER TRANSLATION/RNA 10-OCT-13 2MFC TITLE CSR/RSM PROTEIN-RNA RECOGNITION - A MOLECULAR AFFINITY RULER: TITLE 2 RSMZ(SL1)/RSME(DIMER) 2:1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CARBON STORAGE REGULATOR HOMOLOG; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: SL1(RSMZ) RNA; COMPND 7 CHAIN: B, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS FLUORESCENS; SOURCE 3 ORGANISM_TAXID: 294; SOURCE 4 GENE: RSME, CSRA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET28A; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES KEYWDS CSRA, RSMA, RSME, RSMZ, CSRB, TRANSLATION REPRESSOR PROTEIN, KEYWDS 2 TRANSLATION ACTIVATION, PROTEIN SEQUESTRATION, BACTERIAL PROTEIN, KEYWDS 3 NON-CODING RNA, SRNA, PSEUDOMONAS AERUGINOSA, RNA-BINDING PROTEINS, KEYWDS 4 MESSENGER RNA, MODULATION OF BINDING AFFINITY, MOLECULAR MIMICRY, KEYWDS 5 TRANSLATION-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.DUSS,N.DIARRA DIT KONTE,E.MICHEL,M.SCHUBERT,F.H.-T.ALLAIN REVDAT 3 14-MAY-14 2MFC 1 JRNL REVDAT 2 26-MAR-14 2MFC 1 JRNL REVDAT 1 26-FEB-14 2MFC 0 JRNL AUTH O.DUSS,E.MICHEL,N.DIARRA DIT KONTE,M.SCHUBERT,F.H.ALLAIN JRNL TITL MOLECULAR BASIS FOR THE WIDE RANGE OF AFFINITY FOUND IN JRNL TITL 2 CSR/RSM PROTEIN-RNA RECOGNITION. JRNL REF NUCLEIC ACIDS RES. V. 42 5332 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24561806 JRNL DOI 10.1093/NAR/GKU141 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MFC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-14. REMARK 100 THE RCSB ID CODE IS RCSB103560. 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 SL1(RSMZ), 0.05 MM POTASSIUM REMARK 210 PHOSPHATE, 0.03 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O; 1 MM [U REMARK 210 -100% 15N] RSME, 1 MM SL1(RSMZ), REMARK 210 0.05 MM POTASSIUM PHOSPHATE, 0.03 REMARK 210 MM SODIUM CHLORIDE, 100% D2O; 1 REMARK 210 MM [U-100% 13C; U-100% 15N] RSME, REMARK 210 1 MM SL1(RSMZ), 0.05 MM POTASSIUM REMARK 210 PHOSPHATE, 0.03 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O; 1 MM [U REMARK 210 -100% 13C; U-100% 15N] RSME, 1 MM REMARK 210 SL1(RSMZ), 0.05 MM POTASSIUM REMARK 210 PHOSPHATE, 0.03 MM SODIUM REMARK 210 CHLORIDE, 100% D2O; 1 MM [U-100% REMARK 210 15N] RSME, 1 MM [U-100% 13C; U- REMARK 210 100% 15N]-ADE/URA RNA SL1(RSMZ), REMARK 210 0.05 MM POTASSIUM PHOSPHATE, 0.03 REMARK 210 MM SODIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 1 MM [U-100% 15N] RSME, 1 MM REMARK 210 [U-100% 13C; U-100% 15N]-ADE/URA REMARK 210 RNA SL1(RSMZ), 0.05 MM POTASSIUM REMARK 210 PHOSPHATE, 0.03 MM SODIUM REMARK 210 CHLORIDE, 100% D2O; 1 MM [U-100% REMARK 210 15N] RSME, 1 MM [U-100% 13C; U- REMARK 210 100% 15N]-CYT/GUA RNA SL1(RSMZ), REMARK 210 0.05 MM POTASSIUM PHOSPHATE, 0.03 REMARK 210 MM SODIUM CHLORIDE, 95% H2O/5% REMARK 210 D2O; 1 MM [U-100% 15N] RSME, 1 MM REMARK 210 [U-100% 13C; U-100% 15N]-CYT/GUA REMARK 210 RNA SL1(RSMZ), 0.05 MM POTASSIUM REMARK 210 PHOSPHATE, 0.03 MM SODIUM REMARK 210 CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 2D 1H-1H NOESY; 2D 1H-13C HSQC; REMARK 210 3D 1H-13C NOESY ALIPHATIC; 3D REMARK 210 1FE3FF NOESY; 3D HCCH-TOCSY; 3D REMARK 210 HNCA; 3D HNCACB; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 700 MHZ; 900 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 999 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 1-20 REMARK 465 RES C SSSEQI 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 LYS C 60 REMARK 465 ARG C 61 REMARK 465 GLU C 62 REMARK 465 THR C 63 REMARK 465 PRO C 64 REMARK 465 HIS C 65 REMARK 465 HIS C 66 REMARK 465 HIS C 67 REMARK 465 HIS C 68 REMARK 465 HIS C 69 REMARK 465 HIS C 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 16 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.9 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 THR A 56 -2.67 -146.56 REMARK 500 1 PRO A 58 171.24 -54.71 REMARK 500 1 LEU C 55 160.39 63.68 REMARK 500 1 ALA C 57 44.80 -154.03 REMARK 500 2 PRO A 58 178.01 -55.02 REMARK 500 2 LEU C 55 164.40 63.06 REMARK 500 2 PRO C 58 -171.76 -53.71 REMARK 500 3 THR A 56 1.84 -152.38 REMARK 500 3 PRO A 58 175.38 -52.06 REMARK 500 3 SER C 26 89.24 -152.65 REMARK 500 3 THR C 56 16.77 -148.14 REMARK 500 3 PRO C 58 171.16 -52.46 REMARK 500 4 PRO A 58 171.25 -53.07 REMARK 500 4 THR C 56 -5.84 -144.46 REMARK 500 4 ALA C 57 62.62 -156.53 REMARK 500 5 LEU A 55 167.79 61.16 REMARK 500 5 THR A 56 -3.57 -153.92 REMARK 500 5 PRO A 58 176.09 -54.23 REMARK 500 5 ALA C 57 59.58 -152.60 REMARK 500 6 ALA A 57 82.60 61.21 REMARK 500 6 PRO A 58 167.79 -49.75 REMARK 500 6 LEU C 55 -165.66 -164.52 REMARK 500 6 PRO C 58 171.94 -51.40 REMARK 500 7 THR A 56 -0.28 -142.05 REMARK 500 7 ALA A 57 59.14 -153.23 REMARK 500 7 PRO A 58 172.14 -52.94 REMARK 500 7 LEU C 55 163.57 63.12 REMARK 500 7 PRO C 58 -171.99 -53.71 REMARK 500 8 ALA A 57 58.30 -150.96 REMARK 500 8 LEU C 55 161.90 63.38 REMARK 500 8 ALA C 57 51.18 -148.12 REMARK 500 9 ALA A 57 58.28 -142.17 REMARK 500 9 THR C 56 -0.88 -143.50 REMARK 500 9 ALA C 57 64.58 -154.23 REMARK 500 9 PRO C 58 170.91 -51.27 REMARK 500 10 PRO A 58 177.39 -55.86 REMARK 500 10 GLU C 10 -169.37 -110.94 REMARK 500 10 THR C 56 -0.53 -148.53 REMARK 500 10 ALA C 57 55.09 -150.73 REMARK 500 11 THR A 56 20.54 -154.38 REMARK 500 11 LEU C 55 -179.32 -53.72 REMARK 500 11 THR C 56 17.34 -140.50 REMARK 500 12 ALA A 57 57.23 -144.26 REMARK 500 12 ALA C 57 39.32 -151.22 REMARK 500 13 GLU C 10 -168.04 -121.73 REMARK 500 13 ALA C 57 56.84 -153.19 REMARK 500 14 PRO A 58 171.99 -53.65 REMARK 500 14 LEU C 55 164.50 62.72 REMARK 500 14 ALA C 57 59.59 -146.04 REMARK 500 14 PRO C 58 -168.83 -54.37 REMARK 500 REMARK 500 THIS ENTRY HAS 80 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 2 A B 12 0.06 SIDE CHAIN REMARK 500 5 C B 4 0.09 SIDE CHAIN REMARK 500 5 A D 12 0.07 SIDE CHAIN REMARK 500 6 A D 12 0.06 SIDE CHAIN REMARK 500 10 A D 12 0.07 SIDE CHAIN REMARK 500 11 C B 4 0.08 SIDE CHAIN REMARK 500 12 C B 4 0.07 SIDE CHAIN REMARK 500 12 C D 7 0.07 SIDE CHAIN REMARK 500 12 A D 12 0.06 SIDE CHAIN REMARK 500 14 C D 7 0.07 SIDE CHAIN REMARK 500 15 A B 12 0.06 SIDE CHAIN REMARK 500 16 C B 7 0.08 SIDE CHAIN REMARK 500 17 A D 12 0.06 SIDE CHAIN REMARK 500 18 C D 7 0.09 SIDE CHAIN REMARK 500 18 A D 12 0.07 SIDE CHAIN REMARK 500 19 C D 7 0.06 SIDE CHAIN REMARK 500 20 C B 7 0.08 SIDE CHAIN REMARK 500 20 A D 12 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19544 RELATED DB: BMRB DBREF 2MFC A 1 59 UNP Q5MXB2 Q5MXB2_PSEFL 1 59 DBREF 2MFC C 1 59 UNP Q5MXB2 Q5MXB2_PSEFL 1 59 DBREF 2MFC B -3 19 PDB 2MFC 2MFC -3 19 DBREF 2MFC D -3 19 PDB 2MFC 2MFC -3 19 SEQADV 2MFC LYS A 60 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC ARG A 61 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC GLU A 62 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC THR A 63 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC PRO A 64 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS A 65 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS A 66 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS A 67 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS A 68 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS A 69 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS A 70 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC LYS C 60 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC ARG C 61 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC GLU C 62 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC THR C 63 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC PRO C 64 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS C 65 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS C 66 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS C 67 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS C 68 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS C 69 UNP Q5MXB2 EXPRESSION TAG SEQADV 2MFC HIS C 70 UNP Q5MXB2 EXPRESSION TAG 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 22 G G G U G U C G A C G G A SEQRES 2 B 22 U A G A C A C C C SEQRES 1 C 70 MET LEU ILE LEU THR ARG LYS VAL GLY GLU SER ILE ASN SEQRES 2 C 70 ILE GLY ASP ASP ILE THR ILE THR ILE LEU GLY VAL SER SEQRES 3 C 70 GLY GLN GLN VAL ARG ILE GLY ILE ASN ALA PRO LYS ASP SEQRES 4 C 70 VAL ALA VAL HIS ARG GLU GLU ILE TYR GLN ARG ILE GLN SEQRES 5 C 70 ALA GLY LEU THR ALA PRO ASP LYS ARG GLU THR PRO HIS SEQRES 6 C 70 HIS HIS HIS HIS HIS SEQRES 1 D 22 G G G U G U C G A C G G A SEQRES 2 D 22 U A G A C A C C C HELIX 1 1 GLU A 45 GLN A 52 1 8 HELIX 2 2 GLU C 45 GLN C 52 1 8 SHEET 1 A 5 LEU A 2 LYS A 7 0 SHEET 2 A 5 GLN C 29 ASN C 35 -1 O ILE C 34 N LEU A 2 SHEET 3 A 5 ILE C 18 SER C 26 -1 N THR C 21 O GLY C 33 SHEET 4 A 5 SER C 11 ILE C 14 -1 N ILE C 12 O ILE C 20 SHEET 5 A 5 VAL A 42 ARG A 44 -1 N HIS A 43 O ASN C 13 SHEET 1 B 5 LEU C 2 THR C 5 0 SHEET 2 B 5 GLN A 29 ASN A 35 -1 N ILE A 32 O LEU C 4 SHEET 3 B 5 ILE A 18 SER A 26 -1 N THR A 21 O GLY A 33 SHEET 4 B 5 SER A 11 ILE A 14 -1 N ILE A 12 O ILE A 20 SHEET 5 B 5 VAL C 42 ARG C 44 -1 O HIS C 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