HEADER HYDROLASE/RNA 14-SEP-10 2L3J TITLE THE SOLUTION STRUCTURE OF THE ADAR2 DSRBM-RNA COMPLEX REVEALS A TITLE 2 SEQUENCE-SPECIFIC READ OUT OF THE MINOR GROOVE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE-STRANDED RNA-SPECIFIC EDITASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 74-301; 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 (71-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: PET30-GB1; 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: T7 BACTERIOPHAGE; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 10760 KEYWDS EDITING, DSRNA RECOGNITION, DSRBM, HYDROLASE-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR R.STEFL,F.C.OBERSTRASS,F.H.-T.ALLAIN REVDAT 2 01-MAY-24 2L3J 1 REMARK SEQADV REVDAT 1 27-OCT-10 2L3J 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 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000101911. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.6 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] ENTITY_1-1, 1 REMARK 210 MM RNA (71-MER)-2, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N TROSY REMARK 210 TEMP COMPENSATED REMARK 210 SPECTROMETER FIELD STRENGTH : 900 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 : 19 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: 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: 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. = -9.7 DEGREES REMARK 500 1 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 2 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 4 PRO A 1 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 4 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 PRO A 1 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 5 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 6 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 7 PRO A 1 CA - N - CD ANGL. DEV. = -9.1 DEGREES REMARK 500 7 G B 286 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 8 PRO A 1 CA - N - CD ANGL. DEV. = -10.3 DEGREES REMARK 500 8 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 9 PRO A 1 CA - N - CD ANGL. DEV. = -10.0 DEGREES REMARK 500 9 U B 259 O4' - C1' - N1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 PRO A 1 CA - N - CD ANGL. DEV. = -10.3 DEGREES REMARK 500 10 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 11 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 11 G B 286 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 12 PRO A 1 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 12 U B 259 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 12 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 13 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 13 A B 274 N9 - C1' - C2' ANGL. DEV. = 9.3 DEGREES REMARK 500 13 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 14 PRO A 1 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 14 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 15 PRO A 1 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 15 U B 259 O4' - C1' - N1 ANGL. DEV. = 4.3 DEGREES REMARK 500 15 G B 286 O4' - C1' - N9 ANGL. DEV. = 5.0 DEGREES REMARK 500 16 PRO A 1 CA - N - CD ANGL. DEV. = -9.9 DEGREES REMARK 500 16 U B 241 O4' - C1' - N1 ANGL. DEV. = 4.4 DEGREES REMARK 500 16 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.7 DEGREES REMARK 500 17 PRO A 1 CA - N - CD ANGL. DEV. = -10.2 DEGREES REMARK 500 17 U B 259 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 18 PRO A 1 CA - N - CD ANGL. DEV. = -9.5 DEGREES REMARK 500 18 G B 286 O4' - C1' - N9 ANGL. DEV. = 4.6 DEGREES REMARK 500 19 PRO A 1 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 19 A B 274 N9 - C1' - C2' ANGL. DEV. = 8.4 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 LYS A 17 102.07 -45.55 REMARK 500 1 LEU A 20 172.55 -59.73 REMARK 500 1 SER A 26 -118.50 46.52 REMARK 500 1 GLN A 27 78.24 63.00 REMARK 500 1 ASN A 43 9.67 50.88 REMARK 500 1 THR A 53 154.14 57.85 REMARK 500 1 LYS A 55 -70.67 -58.52 REMARK 500 1 PHE A 72 59.10 -145.92 REMARK 500 1 SER A 76 3.73 -158.13 REMARK 500 1 LEU A 80 16.21 -142.06 REMARK 500 1 ASN A 89 22.33 -70.68 REMARK 500 1 ALA A 97 18.77 -144.09 REMARK 500 1 ASP A 101 11.23 -153.48 REMARK 500 1 PHE A 117 16.42 -142.51 REMARK 500 1 ASP A 124 12.06 -154.48 REMARK 500 1 ASP A 125 29.28 -142.73 REMARK 500 1 PHE A 127 20.69 -147.28 REMARK 500 1 ASP A 132 6.54 -157.72 REMARK 500 1 SER A 134 8.07 -151.26 REMARK 500 1 PRO A 139 166.35 -48.30 REMARK 500 1 PRO A 141 -179.86 -68.05 REMARK 500 1 SER A 143 13.10 -140.30 REMARK 500 1 PRO A 147 150.13 -47.90 REMARK 500 1 PRO A 150 2.97 -58.59 REMARK 500 1 SER A 159 10.99 -143.80 REMARK 500 1 ARG A 171 68.09 -160.66 REMARK 500 1 SER A 180 170.90 -50.37 REMARK 500 1 SER A 182 23.81 -140.25 REMARK 500 1 ALA A 187 26.21 44.61 REMARK 500 1 SER A 189 65.69 -150.41 REMARK 500 1 ASP A 197 3.25 55.97 REMARK 500 1 LEU A 228 -0.63 -144.10 REMARK 500 1 HIS A 232 8.52 -157.93 REMARK 500 1 HIS A 233 20.00 -145.23 REMARK 500 2 PRO A 3 0.93 -55.05 REMARK 500 2 LEU A 5 63.02 -159.02 REMARK 500 2 SER A 26 -120.28 48.34 REMARK 500 2 GLN A 27 80.73 71.66 REMARK 500 2 ASN A 43 6.19 55.82 REMARK 500 2 LYS A 55 -71.63 -59.41 REMARK 500 2 PHE A 72 46.84 -149.98 REMARK 500 2 ASN A 74 -33.01 -163.75 REMARK 500 2 GLU A 77 20.79 -143.68 REMARK 500 2 THR A 85 18.76 -149.21 REMARK 500 2 ASN A 89 24.12 -144.70 REMARK 500 2 GLN A 96 11.20 -142.71 REMARK 500 2 PRO A 100 6.81 -56.03 REMARK 500 2 PHE A 104 -179.22 -68.94 REMARK 500 2 PHE A 107 -8.55 -154.44 REMARK 500 2 SER A 113 12.08 -142.21 REMARK 500 REMARK 500 THIS ENTRY HAS 558 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 4 C B 271 0.06 SIDE CHAIN REMARK 500 8 C B 271 0.09 SIDE CHAIN REMARK 500 8 A B 273 0.06 SIDE CHAIN REMARK 500 9 C B 271 0.06 SIDE CHAIN REMARK 500 12 C B 271 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2L3J A 1 228 UNP P51400 RED1_RAT 74 301 DBREF 2L3J B 237 307 PDB 2L3J 2L3J 237 307 SEQADV 2L3J LEU A 229 UNP P51400 EXPRESSION TAG SEQADV 2L3J GLU A 230 UNP P51400 EXPRESSION TAG SEQADV 2L3J HIS A 231 UNP P51400 EXPRESSION TAG SEQADV 2L3J HIS A 232 UNP P51400 EXPRESSION TAG SEQADV 2L3J HIS A 233 UNP P51400 EXPRESSION TAG SEQADV 2L3J HIS A 234 UNP P51400 EXPRESSION TAG SEQADV 2L3J HIS A 235 UNP P51400 EXPRESSION TAG SEQADV 2L3J HIS A 236 UNP P51400 EXPRESSION TAG SEQRES 1 A 236 PRO GLY PRO VAL LEU PRO LYS ASN ALA LEU MET GLN LEU SEQRES 2 A 236 ASN GLU ILE LYS PRO GLY LEU GLN TYR MET LEU LEU SER SEQRES 3 A 236 GLN THR GLY PRO VAL HIS ALA PRO LEU PHE VAL MET SER SEQRES 4 A 236 VAL GLU VAL ASN GLY GLN VAL PHE GLU GLY SER GLY PRO SEQRES 5 A 236 THR LYS LYS LYS ALA LYS LEU HIS ALA ALA GLU LYS ALA SEQRES 6 A 236 LEU ARG SER PHE VAL GLN PHE PRO ASN ALA SER GLU ALA SEQRES 7 A 236 HIS LEU ALA MET GLY ARG THR LEU SER VAL ASN THR ASP SEQRES 8 A 236 PHE THR SER ASP GLN ALA ASP PHE PRO ASP THR LEU PHE SEQRES 9 A 236 ASN GLY PHE GLU THR PRO ASP LYS SER GLU PRO PRO PHE SEQRES 10 A 236 TYR VAL GLY SER ASN GLY ASP ASP SER PHE SER SER SER SEQRES 11 A 236 GLY ASP VAL SER LEU SER ALA SER PRO VAL PRO ALA SER SEQRES 12 A 236 LEU THR GLN PRO PRO LEU PRO ILE PRO PRO PRO PHE PRO SEQRES 13 A 236 PRO PRO SER GLY LYS ASN PRO VAL MET ILE LEU ASN GLU SEQRES 14 A 236 LEU ARG PRO GLY LEU LYS TYR ASP PHE LEU SER GLU SER SEQRES 15 A 236 GLY GLU SER HIS ALA LYS SER PHE VAL MET SER VAL VAL SEQRES 16 A 236 VAL ASP GLY GLN PHE PHE GLU GLY SER GLY ARG ASN LYS SEQRES 17 A 236 LYS LEU ALA LYS ALA ARG ALA ALA GLN SER ALA LEU ALA SEQRES 18 A 236 THR VAL PHE ASN LEU HIS LEU LEU GLU HIS HIS HIS HIS SEQRES 19 A 236 HIS HIS SEQRES 1 B 71 G G C A U U A A G G U G G SEQRES 2 B 71 G U G G A A U A G U A U A SEQRES 3 B 71 A C A A U A U G C U A A A SEQRES 4 B 71 U G U U G U U A U A G U A SEQRES 5 B 71 U C C C A C C U A C C C U SEQRES 6 B 71 G A U G C C HELIX 1 1 PRO A 6 LYS A 17 1 12 HELIX 2 2 PRO A 52 VAL A 70 1 19 HELIX 3 3 ASN A 162 ARG A 171 1 10 HELIX 4 4 ASN A 207 PHE A 224 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 VAL A 37 N LEU A 25 SHEET 3 A 3 GLN A 45 GLY A 51 -1 O GLN A 45 N VAL A 42 SHEET 1 B 3 LEU A 174 LEU A 179 0 SHEET 2 B 3 PHE A 190 VAL A 196 -1 O VAL A 191 N LEU A 179 SHEET 3 B 3 GLN A 199 GLY A 205 -1 O GLY A 203 N MET A 192 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