10 20 30 40 50 60 70 80 1YNE - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER RNA 24-JAN-05 1YNE
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 APOB 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 1YNE 1 VERSN REVDAT 2 24-MAY-05 1YNE 1 DBREF REVDAT 1 08-FEB-05 1YNE 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 : AMBER 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 1YNE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031714.
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 EDITED APOB RNA SL31;10 REMARK 210 MM NAH2HPO4 ADJUSTED AT PH REMARK 210 5.8; NATURAL ABUNDANCE REMARK 210 LABELING; 90% H2O, 10% D2O AND REMARK 210 ONLY 99.98% D2O; 1.5 MM EDITED REMARK 210 APOB 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, 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 : 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 : 18 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 6 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 U A 18 C5' - C4' - C3' ANGL. DEV. = -9.0 DEGREES REMARK 500 1 U A 18 C3' - C2' - C1' ANGL. DEV. = 4.9 DEGREES REMARK 500 2 U A 4 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 A A 10 C5' - C4' - C3' ANGL. DEV. = -9.1 DEGREES REMARK 500 2 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 2 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 2 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 U A 11 C5' - C4' - C3' ANGL. DEV. = -8.5 DEGREES REMARK 500 3 A A 12 C5' - C4' - C3' ANGL. DEV. = -8.7 DEGREES REMARK 500 3 A A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 4 U A 6 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 A A 10 C5' - C4' - C3' ANGL. DEV. = -9.2 DEGREES REMARK 500 4 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 4 A A 14 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 A A 20 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 C A 22 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 4 A A 23 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 G A 24 N1 - C6 - O6 ANGL. DEV. = -4.2 DEGREES REMARK 500 4 A A 26 C5 - C6 - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 A A 28 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 U A 29 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 A A 26 C5' - C4' - C3' ANGL. DEV. = -9.1 DEGREES REMARK 500 7 G A 2 O4' - C1' - N9 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 G A 2 N1 - C6 - O6 ANGL. DEV. = -3.7 DEGREES REMARK 500 7 A A 3 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 A A 3 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 U A 4 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 7 A A 5 C5 - C6 - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 U A 6 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 7 U A 8 O4' - C1' - N1 ANGL. DEV. = 5.3 DEGREES REMARK 500 7 A A 10 C5 - C6 - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 U A 11 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 A A 12 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 7 A A 12 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 7 A A 12 C5 - C6 - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 U A 13 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 7 A A 14 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 7 A A 14 C4 - C5 - C6 ANGL. DEV. = -3.4 DEGREES REMARK 500 7 A A 14 C5 - C6 - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 A A 14 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 7 A A 15 C4 - C5 - C6 ANGL. DEV. = -3.1 DEGREES REMARK 500 7 A A 15 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 281 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 18 0.07 SIDE_CHAIN REMARK 500 1 A A 23 0.07 SIDE_CHAIN REMARK 500 2 A A 23 0.06 SIDE_CHAIN REMARK 500 7 U A 25 0.08 SIDE_CHAIN REMARK 500 18 G A 19 0.08 SIDE_CHAIN REMARK 500 18 A A 26 0.06 SIDE_CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YLG RELATED DB: PDB REMARK 900 UNEDITED APOB MRNA STRUCTURE (G19 ANTI CONFORMATION) REMARK 900 RELATED ID: 1YNC RELATED DB: PDB REMARK 900 UNEDITED APOB MRNA STRUCTURE (G19 SYN CONFORMATION) REMARK 900 RELATED ID: 1YNG RELATED DB: PDB REMARK 900 EDITED APOB MRNA STRUCTURE (G19 SYN CONFORMATION)
REMARK 999 REMARK 999 SEQUENCE THIS ENTRY 1YNE HAS EDITED RNA WITH U6666 IN ANTI REMARK 999 CONFORMATION. THE EDITED APOB MRNA SEQUENCE LEADING TO THE REMARK 999 TRUNCATED PROTEIN HAS THE SAME ACCESSION NUMBER SINCE IT COMES REMARK 999 FROM THE SAME GENE. THE NUMBERING STARTS AT 6656 ON THE APOB REMARK 999 MRNA SEQUENCE BUT FOR EXPERIMENTAL REASON THE FIRST AND LAST TWO REMARK 999 NUCLEOTIDES GG AND CC WERE ADDED, WHICH DO NOT BELONG TO THE REMARK 999 NATIVE SEQUENCE, THE NUMBER STARTS AT 6654.
DBREF 1YNE A 3 29 GB 4502152 NM_000384 6656 6682
SEQADV 1YNE G A 1 GB 4502152 SEE REMARK 999 SEQADV 1YNE G A 2 GB 4502152 SEE REMARK 999 SEQADV 1YNE U A 13 GB 4502152 C 6666 SEE REMARK 999 SEQADV 1YNE C A 30 GB 4502152 SEE REMARK 999 SEQADV 1YNE C A 31 GB 4502152 SEE REMARK 999
SEQRES 1 A 31 G G A U A U A U G A U A U 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