HEADER RNA 19-JAN-05 1YLG TITLE NMR STRUCTURE OF THE APOB MRNA STEM-LOOP AND ITS INTERACTION WITH THE TITLE 2 C TO U EDITING APOBEC1 COMPLEMENTARY 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 SEQUENCE OF SOURCE 4 THIS RNA NATURALLY EXISTS IN HOMO SAPIENS (HUMAN) KEYWDS RNA EDITING, APOB MRNA, APOBEC1, ACF, RNA EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.MARIS,J.MASSE,F.H.ALLAIN,A.CHESTER,N.NAVARATNAM REVDAT 4 02-MAR-22 1YLG 1 REMARK 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 INTERACTION JRNL TITL 2 WITH THE C TO U EDITING APOBEC1 COMPLEMENTARY FACTOR. JRNL REF RNA V. 11 173 2005 JRNL REFN ISSN 1355-8382 JRNL PMID 15659357 JRNL DOI 10.1261/RNA.7190705 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0, AMBER7 7 REMARK 3 AUTHORS : GUENTERT, P. (CYANA), PONDER, J.W. AND CASE, D.A. REMARK 3 (AMBER7) 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 DEPOSITION ID IS D_1000031652. 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; 90% REMARK 210 H2O, 10% D2O AND ONLY 99.98% D2O; REMARK 210 1.2 MM APOB RNA SL31; 10 MM REMARK 210 NAH2HPO4 ADJUSTED AT PH 5.8; REMARK 210 SELECTIVE U 15N&13C LABELING; 90% REMARK 210 H2O, 10% D2O AND ONLY 99.98% REMARK 210 D2O; 1.0 MMAPOB RNA SL31; 10 MM REMARK 210 NAH2HPO4 ADJUSTED AT PH 5.8; REMARK 210 SELECTIVE A 15N&13C LABELING; 90% REMARK 210 H2O, 10% D2O AND ONLY 99.98% REMARK 210 D2O; 1.0 MM APOB RNA SL31; 10 MM REMARK 210 NAH2HPO4 ADJUSTED AT PH 5.8; REMARK 210 SELECTIVE G&C 15N&13C LABELING; REMARK 210 90% H2O, 10% D2O AND ONLY 99.98% REMARK 210 D2O; 1.5 MM APOB RNA SL31; 10 MM REMARK 210 NAH2HPO4 ADJUSTED AT PH 5.8; REMARK 210 FULL 15N&C13 LABELING; 90% H2O, REMARK 210 10% D2O AND ONLY 99.98% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; 3D_13C REMARK 210 -SEPARATED_NOESY; DQF-COSY; HNN_ REMARK 210 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 : XWINNMR 2004, SPARKY 2002, X REMARK 210 -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 WITH REMARK 210 EXPERIMENTAL NOESY SPECTRUM, REMARK 210 STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES REMARK 210 WITH THE LOWEST 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 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 HO2' G A 9 OP1 A A 10 1.57 REMARK 500 HO2' U A 21 OP1 C A 22 1.58 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 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. = 4.5 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. = 3.1 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. = 4.5 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. = 4.3 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. = 3.1 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 MODEL 1