PDB Short entry for 2MXY HEADER RNA BINDING PROTEIN/RNA 19-JAN-15 2MXY TITLE SOLUTION STRUCTURE OF HNRNP C RRM IN COMPLEX WITH 5'-AUUUUUC-3' RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEINS C1/C2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM (UNP RESIDUES 2-106); COMPND 5 SYNONYM: HNRNP C1/C2, HNRNP_C; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-R(*AP*UP*UP*UP*UP*UP*C)-3'; COMPND 9 CHAIN: B; COMPND 10 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: HNRNPC, HNRPC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTYB11; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS HNRNP C, RRM, COMPLEX, RNA BINDING PROTEIN-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Z.CIENIKOVA,F.F.DAMBERGER,J.HALL,F.H.-T.ALLAIN,C.MARIS REVDAT 1 25-FEB-15 2MXY 0 JRNL AUTH Z.CIENIKOVA,F.F.DAMBERGER,J.HALL,F.H.ALLAIN,C.MARIS JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHTS INTO POLY(URIDINE) TRACT JRNL TITL 2 RECOGNITION BY THE HNRNP C RNA RECOGNITION MOTIF. JRNL REF J.AM.CHEM.SOC. V. 136 14536 2014 JRNL REFN ISSN 0002-7863 JRNL PMID 25216038 JRNL DOI 10.1021/JA507690D REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9, CYANA REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN (AMBER), GUNTERT, REMARK 3 MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FF99SB FORCE-FIELD REMARK 4 REMARK 4 2MXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JAN-15. REMARK 100 THE RCSB ID CODE IS RCSB104183. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.040 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 15N] HNRNP C, 1.0 REMARK 210 MM 5'-R(*AP*UP*UP*UP*UP*UP*C)-3', REMARK 210 20 MM SODIUM PHOSPHATE, 10 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O; REMARK 210 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 HNRNP C, 1.0 MM 5'-R(*AP*UP*UP* REMARK 210 UP*UP*UP*C)-3', 20 MM SODIUM REMARK 210 PHOSPHATE, 10 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O; 1.0 MM [U-100% REMARK 210 13C; U-100% 15N] HNRNP C, 1.0 MM REMARK 210 5'-R(*AP*UP*UP*UP*UP*UP*C)-3', 20 REMARK 210 MM SODIUM PHOSPHATE, 10 MM SODIUM REMARK 210 CHLORIDE, 100% D2O; 0.5-1.0 MM [U REMARK 210 -100% 15N] HNRNP C, 0.5-1.0 MM REMARK 210 [100% 13C5]-URA 5'-R(*AP*UP*UP* REMARK 210 UP*UP*UP*C)-3', 20 MM SODIUM REMARK 210 PHOSPHATE, 10 MM SODIUM CHLORIDE, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HNCO; 3D 1H-15N NOESY; 3D HCCH- REMARK 210 TOCSY; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 3D 1H-13C EDITED-FILTERED NOESY; REMARK 210 2D 1H-13C HSQC; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 600 MHZ; 700 MHZ; 500 REMARK 210 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVIII REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 U B 2 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 1 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C B 7 O4' - C1' - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 2 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 U B 6 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 3 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 4 A B 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 4 U B 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 C B 7 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 5 A B 1 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 5 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 6 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 6 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 6 U B 6 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 7 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 8 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 8 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 9 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 9 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 10 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 10 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 11 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 11 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 11 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 11 C B 7 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 12 A B 1 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 12 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 13 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 13 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 13 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 14 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 14 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 14 U B 6 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 15 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 16 U B 3 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 16 U B 4 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 16 C B 7 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 17 A B 1 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 59 ANGLE DEVIATIONS. 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 6 16.61 -149.97 REMARK 500 1 ALA A 76 13.66 51.32 REMARK 500 1 LYS A 94 9.30 57.46 REMARK 500 1 ALA A 95 -15.63 -153.96 REMARK 500 2 THR A 6 10.76 -148.69 REMARK 500 2 ASN A 22 19.01 56.50 REMARK 500 2 THR A 25 9.77 52.95 REMARK 500 2 ALA A 76 14.84 52.84 REMARK 500 2 LYS A 94 5.61 59.20 REMARK 500 2 ALA A 95 -18.08 -152.53 REMARK 500 3 THR A 6 17.86 -148.18 REMARK 500 3 PRO A 11 0.74 -66.24 REMARK 500 3 ASN A 22 17.85 56.42 REMARK 500 3 THR A 25 8.82 52.73 REMARK 500 3 ALA A 76 15.04 53.49 REMARK 500 3 LYS A 94 6.13 58.75 REMARK 500 4 THR A 6 20.16 -148.54 REMARK 500 4 ALA A 76 18.29 51.64 REMARK 500 4 LYS A 94 -2.24 59.07 REMARK 500 4 ALA A 95 -29.34 -159.88 REMARK 500 5 THR A 6 19.41 -148.66 REMARK 500 5 ASN A 22 16.52 56.18 REMARK 500 5 THR A 25 13.66 49.42 REMARK 500 5 ALA A 76 13.22 55.11 REMARK 500 5 LYS A 94 6.32 58.69 REMARK 500 6 ALA A 76 10.89 52.41 REMARK 500 6 ALA A 101 0.61 -67.55 REMARK 500 7 THR A 6 16.12 -150.08 REMARK 500 7 ASN A 22 19.30 55.09 REMARK 500 7 ALA A 76 17.93 51.74 REMARK 500 7 PRO A 88 29.00 -76.12 REMARK 500 7 ASN A 91 4.76 -67.86 REMARK 500 7 ARG A 92 6.23 54.93 REMARK 500 7 LYS A 94 142.45 59.52 REMARK 500 7 ALA A 95 163.95 57.23 REMARK 500 7 TYR A 105 10.61 52.49 REMARK 500 8 ASN A 7 -128.97 -96.84 REMARK 500 8 LYS A 8 172.85 61.55 REMARK 500 8 THR A 25 7.02 53.34 REMARK 500 8 ALA A 76 19.10 51.85 REMARK 500 8 LYS A 94 178.09 60.66 REMARK 500 9 THR A 6 18.92 -149.59 REMARK 500 9 ASN A 22 17.47 56.03 REMARK 500 9 THR A 25 9.96 51.97 REMARK 500 9 ALA A 76 15.73 52.58 REMARK 500 9 LYS A 94 16.73 56.72 REMARK 500 10 THR A 6 11.76 -148.03 REMARK 500 10 THR A 25 2.59 -64.63 REMARK 500 10 ALA A 76 14.03 52.02 REMARK 500 10 LYS A 94 17.57 55.91 REMARK 500 REMARK 500 THIS ENTRY HAS 109 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 U B 2 0.06 SIDE CHAIN REMARK 500 17 U B 5 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25436 RELATED DB: BMRB DBREF 2MXY A 2 106 UNP P07910 HNRPC_HUMAN 2 106 DBREF 2MXY B 1 7 PDB 2MXY 2MXY 1 7 SEQRES 1 A 105 ALA SER ASN VAL THR ASN LYS THR ASP PRO ARG SER MET SEQRES 2 A 105 ASN SER ARG VAL PHE ILE GLY ASN LEU ASN THR LEU VAL SEQRES 3 A 105 VAL LYS LYS SER ASP VAL GLU ALA ILE PHE SER LYS TYR SEQRES 4 A 105 GLY LYS ILE VAL GLY CYS SER VAL HIS LYS GLY PHE ALA SEQRES 5 A 105 PHE VAL GLN TYR VAL ASN GLU ARG ASN ALA ARG ALA ALA SEQRES 6 A 105 VAL ALA GLY GLU ASP GLY ARG MET ILE ALA GLY GLN VAL SEQRES 7 A 105 LEU ASP ILE ASN LEU ALA ALA GLU PRO LYS VAL ASN ARG SEQRES 8 A 105 GLY LYS ALA GLY VAL LYS ARG SER ALA ALA GLU MET TYR SEQRES 9 A 105 GLY SEQRES 1 B 7 A U U U U U C HELIX 1 1 LYS A 29 PHE A 37 1 9 HELIX 2 2 ASN A 59 ALA A 68 1 10 SHEET 1 A 4 ILE A 43 VAL A 48 0 SHEET 2 A 4 PHE A 52 TYR A 57 -1 O GLN A 56 N GLY A 45 SHEET 3 A 4 ARG A 17 GLY A 21 -1 N VAL A 18 O VAL A 55 SHEET 4 A 4 ASP A 81 LEU A 84 -1 O ASN A 83 N PHE A 19 SHEET 1 B 2 MET A 74 ILE A 75 0 SHEET 2 B 2 GLN A 78 VAL A 79 -1 O GLN A 78 N ILE A 75 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