HEADER RNA BINDING PROTEIN 03-JUL-18 6DZC TITLE SOLUTION STRUCTURE OF RBFOX2 RRM MIMETIC PEPTIDE CPFOX6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CPFOX6; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 36630 KEYWDS PEPTIDOMIMETICS, PEPTIDE STRUCTURE, RNA RECOGNITION, RNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR Y.-T.SUN,G.VARANI REVDAT 2 14-JUN-23 6DZC 1 LINK REVDAT 1 15-MAY-19 6DZC 0 JRNL AUTH Y.T.SUN,M.D.SHORTRIDGE,G.VARANI JRNL TITL A SMALL CYCLIC BETA-HAIRPIN PEPTIDE MIMICS THE RBFOX2 RNA JRNL TITL 2 RECOGNITION MOTIF AND BINDS TO THE PRECURSOR MIRNA 20B. JRNL REF CHEMBIOCHEM V. 20 931 2019 JRNL REFN ESSN 1439-7633 JRNL PMID 30537200 JRNL DOI 10.1002/CBIC.201800645 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6DZC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000234870. 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 : 10 MM POTASSIUM PHOSPHATE, 10 MM REMARK 210 POTASSIUM CHLORIDE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 4.0 MG/ML CPFOX6, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, SPARKY, TOPSPIN 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 LOWEST REMARK 210 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: 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N GLY A 1 C ARG A 16 1.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 5 SER A 2 N SER A 2 CA 0.344 REMARK 500 5 SER A 2 CA SER A 2 CB 0.151 REMARK 500 5 SER A 2 CA SER A 2 C -0.533 REMARK 500 REMARK 500 REMARK: NULL 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 5 SER A 2 CB - CA - C ANGL. DEV. = 27.2 DEGREES REMARK 500 5 SER A 2 N - CA - CB ANGL. DEV. = -21.3 DEGREES REMARK 500 5 SER A 2 CA - CB - OG ANGL. DEV. = 17.5 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 -166.57 56.00 REMARK 500 1 ARG A 3 109.00 55.48 REMARK 500 1 PHE A 5 125.44 173.52 REMARK 500 1 DPR A 8 -97.54 32.88 REMARK 500 1 PRO A 9 10.47 -69.34 REMARK 500 1 ASN A 14 -17.98 -164.54 REMARK 500 1 GLU A 15 40.28 33.00 REMARK 500 2 SER A 2 78.61 -164.63 REMARK 500 2 ARG A 3 125.62 -172.26 REMARK 500 2 DPR A 8 -99.35 34.98 REMARK 500 2 ARG A 13 143.08 175.71 REMARK 500 3 DPR A 8 -98.80 34.27 REMARK 500 4 SER A 2 -170.82 -52.95 REMARK 500 4 DPR A 8 -99.79 35.38 REMARK 500 4 ARG A 13 -149.02 -132.11 REMARK 500 4 GLU A 15 6.39 -179.88 REMARK 500 5 SER A 2 -123.85 -40.98 REMARK 500 5 PHE A 5 124.28 168.40 REMARK 500 5 DPR A 8 -98.46 33.86 REMARK 500 5 ASN A 14 -121.44 -144.67 REMARK 500 5 GLU A 15 0.01 -159.27 REMARK 500 6 ARG A 3 148.42 61.94 REMARK 500 6 DPR A 8 -100.23 36.03 REMARK 500 6 ASN A 14 -168.82 -116.29 REMARK 500 7 SER A 2 -169.05 -63.15 REMARK 500 7 DPR A 8 -98.64 34.04 REMARK 500 7 ARG A 13 143.10 174.22 REMARK 500 7 GLU A 15 -93.38 41.66 REMARK 500 8 SER A 2 39.61 78.00 REMARK 500 8 PHE A 5 118.46 -173.28 REMARK 500 8 DPR A 8 -98.38 33.81 REMARK 500 8 ARG A 13 143.50 176.28 REMARK 500 8 ASN A 14 -133.88 -127.07 REMARK 500 8 GLU A 15 45.53 -168.09 REMARK 500 9 SER A 2 -123.82 -75.92 REMARK 500 9 DPR A 8 -99.98 35.60 REMARK 500 9 ASN A 14 -6.27 -144.43 REMARK 500 10 SER A 2 -132.35 -139.22 REMARK 500 10 PHE A 5 122.80 -173.29 REMARK 500 10 DPR A 8 -99.30 34.78 REMARK 500 10 ASN A 14 -167.29 -127.23 REMARK 500 10 GLU A 15 -179.90 -176.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30489 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF RBFOX2 RRM MIMETIC PEPTIDE CPFOX6 DBREF 6DZC A 1 16 PDB 6DZC 6DZC 1 16 SEQRES 1 A 16 GLY SER ARG GLY PHE ARG PHE DPR PRO LYS ILE ILE ARG SEQRES 2 A 16 ASN GLU ARG HET DPR A 8 14 HETNAM DPR D-PROLINE FORMUL 1 DPR C5 H9 N O2 SHEET 1 AA1 2 PHE A 5 PHE A 7 0 SHEET 2 AA1 2 LYS A 10 ILE A 12 -1 O LYS A 10 N PHE A 7 LINK C PHE A 7 N DPR A 8 1555 1555 1.31 LINK C DPR A 8 N PRO A 9 1555 1555 1.32 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