HEADER HYDROLASE/RNA 12-SEP-10 2L3C TITLE SOLUTION STRUCTURE OF ADAR2 DSRBM1 BOUND TO LSL RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC EDITASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 74-147; COMPND 5 SYNONYM: DSRNA ADENOSINE DEAMINASE, RNA-EDITING DEAMINASE 1, RNA- COMPND 6 EDITING ENZYME 1; COMPND 7 EC: 3.5.-.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (34-MER); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: ADARB1, RED1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET16; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 11 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 12 ORGANISM_TAXID: 10116; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS EDITING, DSRNA RECOGNITION, DSRBM, HYDROLASE-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.ALLAIN,R.STEFL,F.OBERSTRASS REVDAT 2 01-MAY-24 2L3C 1 REMARK REVDAT 1 27-OCT-10 2L3C 0 JRNL AUTH R.STEFL,F.C.OBERSTRASS,J.L.HOOD,M.JOURDAN,M.ZIMMERMANN, JRNL AUTH 2 L.SKRISOVSKA,C.MARIS,L.PENG,C.HOFR,R.B.EMESON,F.H.ALLAIN JRNL TITL THE SOLUTION STRUCTURE OF THE ADAR2 DSRBM-RNA COMPLEX JRNL TITL 2 REVEALS A SEQUENCE-SPECIFIC READOUT OF THE MINOR GROOVE. JRNL REF CELL(CAMBRIDGE,MASS.) V. 143 225 2010 JRNL REFN ISSN 0092-8674 JRNL PMID 20946981 JRNL DOI 10.1016/J.CELL.2010.09.026 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN, AMBER REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLM REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L3C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000101904. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 278 REMARK 210 PH : 7.6; 7.6 REMARK 210 IONIC STRENGTH : 0; 0 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] PROTEIN-1, 1 MM USL REMARK 210 RNA-2, 90% H2O/10% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] PROTEIN-3, REMARK 210 1 MM USL RNA-4, 90% H2O/10% D2O; REMARK 210 1 MM [U-100% 15N] PROTEIN-5, 1 REMARK 210 MM USL RNA-6, 100% D2O; 1 MM [U- REMARK 210 100% 13C; U-100% 15N] PROTEIN-7, REMARK 210 1 MM USL RNA-8, 100% D2O; 1 MM REMARK 210 [U-100% 15N] PROTEIN-9, 1 MM [U- REMARK 210 13C; U-15N]-GUA,URA USL RNA-10, REMARK 210 100% D2O; 1 MM [U-100% 15N] REMARK 210 PROTEIN-11, 1 MM [U-13C; U-15N]- REMARK 210 ADE,CYT USL RNA-12, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 2D 1H-1H TOCSY; 3D HCCH-TOCSY; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D 1H-13C FILTERED-EDITED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 PRO A 1 CA - N - CD ANGL. DEV. = -9.5 DEGREES REMARK 500 1 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 2 PRO A 1 CA - N - CD ANGL. DEV. = -9.5 DEGREES REMARK 500 2 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 3 PRO A 1 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 3 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 4 PRO A 1 CA - N - CD ANGL. DEV. = -10.0 DEGREES REMARK 500 4 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.3 DEGREES REMARK 500 5 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 5 U B 90 C4' - C3' - C2' ANGL. DEV. = -6.2 DEGREES REMARK 500 5 G B 104 O4' - C1' - N9 ANGL. DEV. = 6.1 DEGREES REMARK 500 6 PRO A 1 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 6 U B 80 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 7 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 7 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.6 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -9.5 DEGREES REMARK 500 8 U B 80 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 8 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 9 PRO A 1 CA - N - CD ANGL. DEV. = -9.5 DEGREES REMARK 500 9 G B 104 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 10 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.9 DEGREES REMARK 500 11 PRO A 1 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 11 G B 104 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 12 PRO A 1 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 12 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.7 DEGREES REMARK 500 13 PRO A 1 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 13 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.8 DEGREES REMARK 500 14 G B 104 O4' - C1' - N9 ANGL. DEV. = 6.0 DEGREES REMARK 500 15 PRO A 1 CA - N - CD ANGL. DEV. = -10.1 DEGREES REMARK 500 15 U B 80 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 15 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.1 DEGREES REMARK 500 16 PRO A 1 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 16 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 17 PRO A 1 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 17 G B 104 O4' - C1' - N9 ANGL. DEV. = 6.5 DEGREES REMARK 500 18 PRO A 1 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 18 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 19 PRO A 1 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 19 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 20 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 20 U B 90 C4' - C3' - C2' ANGL. DEV. = -6.0 DEGREES REMARK 500 20 G B 104 O4' - C1' - N9 ANGL. DEV. = 5.9 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 VAL A 4 -173.31 45.85 REMARK 500 1 LEU A 5 54.54 -154.51 REMARK 500 1 PRO A 18 -9.16 -48.51 REMARK 500 1 SER A 26 -133.74 32.37 REMARK 500 1 GLN A 27 87.01 75.98 REMARK 500 1 VAL A 31 -27.41 177.41 REMARK 500 1 THR A 53 174.97 62.75 REMARK 500 1 LYS A 55 -78.74 -55.68 REMARK 500 1 SER A 68 -85.19 -62.77 REMARK 500 1 PHE A 72 64.60 -150.10 REMARK 500 2 LEU A 5 54.53 -150.11 REMARK 500 2 PRO A 18 -13.21 -47.07 REMARK 500 2 SER A 26 161.18 18.04 REMARK 500 2 GLN A 27 72.69 170.78 REMARK 500 2 ASN A 43 15.25 52.09 REMARK 500 2 THR A 53 160.03 62.92 REMARK 500 3 LEU A 5 54.95 -149.93 REMARK 500 3 LYS A 17 85.93 -44.18 REMARK 500 3 SER A 26 161.70 18.20 REMARK 500 3 GLN A 27 75.00 172.36 REMARK 500 3 ASN A 43 25.34 49.65 REMARK 500 3 THR A 53 140.78 64.73 REMARK 500 3 SER A 68 -84.80 -56.48 REMARK 500 3 PHE A 72 64.42 -151.12 REMARK 500 4 VAL A 4 9.51 46.24 REMARK 500 4 LEU A 5 56.77 -154.59 REMARK 500 4 LYS A 17 94.85 -44.75 REMARK 500 4 SER A 26 162.12 18.32 REMARK 500 4 GLN A 27 76.07 170.71 REMARK 500 4 ASN A 43 12.38 50.07 REMARK 500 4 THR A 53 -75.17 65.23 REMARK 500 4 LYS A 54 -32.47 179.25 REMARK 500 5 PRO A 18 5.47 -49.59 REMARK 500 5 SER A 26 161.43 17.51 REMARK 500 5 GLN A 27 74.53 172.31 REMARK 500 5 ASN A 43 19.24 51.33 REMARK 500 5 THR A 53 168.67 63.32 REMARK 500 5 LYS A 55 -79.41 -55.81 REMARK 500 6 LEU A 5 56.42 -156.94 REMARK 500 6 LYS A 17 89.24 -45.61 REMARK 500 6 SER A 26 135.40 -14.87 REMARK 500 6 GLN A 27 76.90 -154.85 REMARK 500 6 ASN A 43 12.17 52.83 REMARK 500 6 LYS A 54 -43.57 68.43 REMARK 500 6 SER A 68 -84.78 -69.58 REMARK 500 7 LEU A 5 58.80 -149.24 REMARK 500 7 LYS A 17 88.60 -44.23 REMARK 500 7 SER A 26 162.25 17.37 REMARK 500 7 GLN A 27 75.69 173.01 REMARK 500 7 ASN A 43 18.01 50.38 REMARK 500 REMARK 500 THIS ENTRY HAS 147 RAMACHANDRAN OUTLIERS. 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 9 G B 104 0.07 SIDE CHAIN REMARK 500 17 G B 104 0.07 SIDE CHAIN REMARK 500 18 G B 104 0.07 SIDE CHAIN REMARK 500 19 G B 104 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L3J RELATED DB: PDB DBREF 2L3C A 1 74 UNP P51400 RED1_RAT 74 147 DBREF 2L3C B 75 108 PDB 2L3C 2L3C 75 108 SEQRES 1 A 74 PRO GLY PRO VAL LEU PRO LYS ASN ALA LEU MET GLN LEU SEQRES 2 A 74 ASN GLU ILE LYS PRO GLY LEU GLN TYR MET LEU LEU SER SEQRES 3 A 74 GLN THR GLY PRO VAL HIS ALA PRO LEU PHE VAL MET SER SEQRES 4 A 74 VAL GLU VAL ASN GLY GLN VAL PHE GLU GLY SER GLY PRO SEQRES 5 A 74 THR LYS LYS LYS ALA LYS LEU HIS ALA ALA GLU LYS ALA SEQRES 6 A 74 LEU ARG SER PHE VAL GLN PHE PRO ASN SEQRES 1 B 34 G G U A G U A U A A C A A SEQRES 2 B 34 U A U C C G U G U U G U U SEQRES 3 B 34 A U A G U A C C HELIX 1 1 PRO A 6 LYS A 17 1 12 HELIX 2 2 THR A 53 VAL A 70 1 18 SHEET 1 A 3 GLN A 21 THR A 28 0 SHEET 2 A 3 LEU A 35 VAL A 42 -1 O SER A 39 N MET A 23 SHEET 3 A 3 GLN A 45 PRO A 52 -1 O GLN A 45 N VAL A 42 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