HEADER RNA 11-MAY-15 2N2O TITLE STRUCTURE OF MURINE TUMOUR NECROSIS FACTOR ALPHA CDE RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(P*GP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*UP COMPND 4 *U)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS CDE, RNA, MURINE, WILD TYPE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR L.CODUTTI,K.LEPPEK,J.ZALESAK,V.WINDEISEN,P.MASIEWICZ,G.STOECKLIN, AUTHOR 2 T.CARLOMAGNO REVDAT 3 14-JUN-23 2N2O 1 REMARK REVDAT 2 26-AUG-15 2N2O 1 JRNL REVDAT 1 05-AUG-15 2N2O 0 JRNL AUTH L.CODUTTI,K.LEPPEK,J.ZALESAK,V.WINDEISEN,P.MASIEWICZ, JRNL AUTH 2 G.STOECKLIN,T.CARLOMAGNO JRNL TITL A DISTINCT, SEQUENCE-INDUCED CONFORMATION IS REQUIRED FOR JRNL TITL 2 RECOGNITION OF THE CONSTITUTIVE DECAY ELEMENT RNA BY ROQUIN. JRNL REF STRUCTURE V. 23 1437 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 26165594 JRNL DOI 10.1016/J.STR.2015.06.001 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N2O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000104345. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.30 MM [U-100% 13C; U-100% 15N] REMARK 210 RNA, 20 MM SODIUM PHOSPHATE, 100% REMARK 210 D2O; 0.30 MM [U-100% 13C; U-100% REMARK 210 15N] RNA, 20 MM SODIUM REMARK 210 PHOSPHATE, 90% H2O/10% D2O; 0.30 REMARK 210 MM [U-100% 13C; U-100% 15N] RNA, REMARK 210 20 MM SODIUM PHOSPHATE, 30 MG/ML REMARK 210 PF1 PHAGE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 IMMINO-1H-1H NOESY; 3D-HCCH-COSY- REMARK 210 TOCSY; 3D HSCNB/HBCNB; 2D HNN- REMARK 210 COSY; 3D 13C-EDITED NOESY; 2D REMARK 210 COSY; 1H-31P HET-COR(P,H-COSY-H, REMARK 210 C-HMQC); T1-13C-EDIT RELAXATION; REMARK 210 T1RHO-13C-EDIT RELAXATION; 13C- REMARK 210 BASE EDITED IPAP; 13C-SUGAR REMARK 210 EDITED IPAP REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CCPN_ANALYSIS 2.3, ARIA REMARK 210 1.2 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 H2' C A 10 H5'' U A 11 1.26 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 3 U A 13 C3' - C2' - C1' ANGL. DEV. = -4.6 DEGREES REMARK 500 6 C A 19 C3' - C2' - C1' ANGL. DEV. = -4.2 DEGREES REMARK 500 9 U A 4 C1' - O4' - C4' ANGL. DEV. = -5.0 DEGREES 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 10 C A 10 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25603 RELATED DB: BMRB REMARK 900 RELATED ID: 2N2P RELATED DB: PDB DBREF 2N2O A 1 23 PDB 2N2O 2N2O 1 23 SEQRES 1 A 23 G C A U G U U U U C U G U SEQRES 2 A 23 G A A A A C G G U U 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