HEADER RNA 19-JAN-05 1YLG TITLE NMR STRUCTURE OF THE APOB MRNA STEM-LOOP AND ITS TITLE 2 INTERACTION WITH THE C TO U EDITING APOBEC1 COMPLEMENTARY TITLE 3 FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOLIPOPROTEIN B MRNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EDITING SITE OF APOBEC-1 ENZYME; COMPND 5 SYNONYM: APOB MRNA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: IN VITRO T7 POLYMERASE TRANSCRIPTION. THE SOURCE 4 SEQUENCE OF THIS RNA NATURALLY EXISTS IN HOMO SAPIENS SOURCE 5 (HUMAN) KEYWDS RNA EDITING, APOB MRNA, APOBEC1, ACF, NMR STRUCTURE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.MARIS,J.MASSE,F.H.ALLAIN,A.CHESTER,N.NAVARATNAM REVDAT 3 24-FEB-09 1YLG 1 VERSN REVDAT 2 08-FEB-05 1YLG 1 JRNL REVDAT 1 01-FEB-05 1YLG 0 JRNL AUTH C.MARIS,J.MASSE,A.CHESTER,N.NAVARATNAM,F.H.ALLAIN JRNL TITL NMR STRUCTURE OF THE APOB MRNA STEM-LOOP AND ITS JRNL TITL 2 INTERACTION WITH THE C TO U EDITING APOBEC1 JRNL TITL 3 COMPLEMENTARY FACTOR. JRNL REF RNA V. 11 173 2005 JRNL REFN ISSN 1355-8382 JRNL PMID 15659357 JRNL DOI 10.1261/RNA.7190705 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER7 7 REMARK 3 AUTHORS : PONDER, J.W. AND CASE, D.A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CALCULATION IN VACUUM CONDITION REMARK 4 REMARK 4 1YLG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031652. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313; 278 REMARK 210 PH : 5.8; 5.8 REMARK 210 IONIC STRENGTH : 10 MM NA2HPO4; 10 MM NA2HPO4 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM APOB RNA SL31;10 MM REMARK 210 NAH2HPO4 ADJUSTED AT PH 5.8; REMARK 210 NATURAL ABUNDANCE LABELING; REMARK 210 90% H2O, 10% D2O AND ONLY REMARK 210 99.98% D2O; 1.2 MM APOB RNA REMARK 210 SL31; 10 MM NAH2HPO4 ADJUSTED REMARK 210 AT PH 5.8; SELECTIVE U 15N&13C REMARK 210 LABELING; 90% H2O, 10% D2O AND REMARK 210 ONLY 99.98% D2O; 1.0 MMAPOB REMARK 210 RNA SL31; 10 MM NAH2HPO4 REMARK 210 ADJUSTED AT PH 5.8; SELECTIVE REMARK 210 A 15N&13C LABELING; 90% H2O, REMARK 210 10% D2O AND ONLY 99.98% D2O; REMARK 210 1.0 MM APOB RNA SL31; 10 MM REMARK 210 NAH2HPO4 ADJUSTED AT PH 5.8; REMARK 210 SELECTIVE G&C 15N&13C REMARK 210 LABELING; 90% H2O, 10% D2O AND REMARK 210 ONLY 99.98% D2O; 1.5 MM APOB REMARK 210 RNA SL31; 10 MM NAH2HPO4 REMARK 210 ADJUSTED AT PH 5.8; FULL 15N& REMARK 210 C13 LABELING; 90% H2O, 10% D2O REMARK 210 AND ONLY 99.98% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY, 3D_13C- REMARK 210 SEPARATED_NOESY, DQF-COSY, REMARK 210 HNN_COSY, HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX, AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0, XWINNMR 2004, REMARK 210 SPARKY 2002, X-EASY 2001 REMARK 210 METHOD USED : CYANA & AMBER7 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BACK CALCULATED DATA AGREE REMARK 210 WITH EXPERIMENTAL NOESY REMARK 210 SPECTRUM,STRUCTURES WITH THE REMARK 210 LEAST RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 12 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 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 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 U A 11 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 1 A A 14 C4 - C5 - C6 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 U A 29 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 3 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 3 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 A A 15 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 3 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 3 U A 16 N3 - C2 - O2 ANGL. DEV. = -4.2 DEGREES REMARK 500 3 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.4 DEGREES REMARK 500 3 A A 23 C5 - C6 - N1 ANGL. DEV. = 4.2 DEGREES REMARK 500 3 A A 26 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 U A 27 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 U A 29 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 5 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 C A 13 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 5 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 5 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 A A 15 N1 - C6 - N6 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 U A 18 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 G A 24 N1 - C6 - O6 ANGL. DEV. = -4.9 DEGREES REMARK 500 5 U A 29 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 A A 7 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 A A 10 C5' - C4' - C3' ANGL. DEV. = -8.7 DEGREES REMARK 500 7 C A 13 C4' - C3' - C2' ANGL. DEV. = -6.5 DEGREES REMARK 500 7 A A 15 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 7 A A 15 C5 - N7 - C8 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 A A 15 N7 - C8 - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 A A 20 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES REMARK 500 7 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 A A 28 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 175 ANGLE DEVIATIONS. 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 A 16 0.08 SIDE_CHAIN REMARK 500 5 A A 15 0.06 SIDE_CHAIN REMARK 500 9 A A 23 0.06 SIDE_CHAIN REMARK 500 10 A A 26 0.06 SIDE_CHAIN REMARK 500 11 A A 7 0.06 SIDE_CHAIN REMARK 500 12 A A 15 0.06 SIDE_CHAIN REMARK 500 12 A A 23 0.06 SIDE_CHAIN REMARK 500 13 A A 15 0.07 SIDE_CHAIN REMARK 500 15 A A 15 0.06 SIDE_CHAIN REMARK 500 17 C A 13 0.06 SIDE_CHAIN REMARK 500 19 A A 15 0.08 SIDE_CHAIN REMARK 500 19 U A 17 0.07 SIDE_CHAIN REMARK 500 20 U A 16 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YNC RELATED DB: PDB REMARK 900 RELATED ID: 1YNE RELATED DB: PDB REMARK 900 RELATED ID: 1YNG RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE EDITED APOB MRNA SEQUENCE LEADING TO THE TRUNCATED REMARK 999 PROTEIN HAS THE SAME ACCESSION NUMBER SINCE IT COMES FROM REMARK 999 THE SAME GENE. THE NUMBERING STARTS AT 6656 ON THE APOB REMARK 999 MRNA SEQUENCE BUT FOR EXPERIMENTAL REASON THE FIRST AND REMARK 999 LAST TWO NUCLEOTIDES GG AND CC WERE ADDED, WHICH DO NOT REMARK 999 BELONG TO THE NATIVE SEQUENCE, THE NUMBER STARTS AT 6654. DBREF 1YLG A 3 29 GB 4502152 NM_000384 6656 6682 SEQADV 1YLG G A 1 GB 4502152 SEE REMARK 999 SEQADV 1YLG G A 2 GB 4502152 SEE REMARK 999 SEQADV 1YLG C A 30 GB 4502152 SEE REMARK 999 SEQADV 1YLG C A 31 GB 4502152 SEE REMARK 999 SEQRES 1 A 31 G G A U A U A U G A U A C SEQRES 2 A 31 A A U U U G A U C A G U A SEQRES 3 A 31 U A U C C 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 185 0 0 0 0 0 0 6 0 0 0 3 END