HEADER HYDROLASE/RNA 20-AUG-10 2L2K TITLE SOLUTION NMR STRUCTURE OF THE R/G STEM LOOP RNA-ADAR2 DSRBM2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSINE DEAMINASE; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: UNP RESIDUES 231-301; COMPND 5 SYNONYM: RNA-SPECIFIC, B1, ISOFORM CRA_D; COMPND 6 EC: 3.5.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (42-MER); COMPND 10 CHAIN: A; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ADAR2, ADARB1, MCG_3378, RED1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET16; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606 KEYWDS AC MISMATCH, RNA EDITING, DSRBM, STEMLOOP, HYDROLASE-RNA COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.H.-T.ALLAIN,F.C.OBERSTRASS,R.STEFL REVDAT 1 27-OCT-10 2L2K 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 : AMBER REMARK 3 AUTHORS : CASE, D.A. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CYANA-AMBER REFINEMENT REMARK 4 REMARK 4 2L2K COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-10. REMARK 100 THE RCSB ID CODE IS RCSB101876. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 7.6 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 15N] COMPLEX-1, 90% REMARK 210 H2O/10% D2O; 1 MM [U-100% 15N] REMARK 210 COMPLEX-2, 100% D2O; 1 MM [U-100% REMARK 210 15N] COMPLEX-3, 90% H2O/10% D2O; REMARK 210 1 MM [U-100% 13C; U-100% 15N] REMARK 210 COMPLEX-4, 100% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N] COMPLEX-5, 100% REMARK 210 D2O; 1 MM [U-100% 13C; U-100% REMARK 210 15N] COMPLEX-6, 100% D2O; 1 MM [U REMARK 210 -100% 13C; U-100% 15N] COMPLEX-7, REMARK 210 100% D2O; 1 MM [U-100% 13C; U- REMARK 210 100% 15N] COMPLEX-8, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D-NOESY-WATER; 2D-NOESY-D2O; REMARK 210 3D_13C-SEPARATED_NOESY; 3D_15N - REMARK 210 SEPARATED_NOESY; 2D 1H-1H TOCSY; REMARK 210 3D 1H-13C NOESY; 2D 1H- 13C HSQC; REMARK 210 2D 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX, AVNACE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.0, CYANA, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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: B, 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' C A 30 H5' A A 31 1.49 REMARK 500 HO2' U A 34 H5' A A 35 1.59 REMARK 500 HO2' U A 39 H5' G A 40 1.59 REMARK 500 HO2' A A 35 H5' C A 36 1.60 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 2 PRO B 43 CA - N - CD ANGL. DEV. = -10.1 DEGREES REMARK 500 4 PRO B 43 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 7 PRO B 43 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 11 PRO B 43 CA - N - CD ANGL. DEV. = -9.3 DEGREES REMARK 500 12 PRO B 43 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 13 PRO B 43 CA - N - CD ANGL. DEV. = -9.8 DEGREES REMARK 500 14 PRO B 43 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 15 PRO B 43 CA - N - CD ANGL. DEV. = -9.7 DEGREES REMARK 500 18 PRO B 43 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 19 PRO B 43 CA - N - CD ANGL. DEV. = -9.6 DEGREES REMARK 500 19 C A 22 O4' - C1' - N1 ANGL. DEV. = 4.3 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 ARG B 56 84.84 -153.46 REMARK 500 1 SER B 65 173.74 -53.57 REMARK 500 1 ALA B 72 18.87 -142.05 REMARK 500 1 ASP B 82 9.53 57.45 REMARK 500 1 LEU B 111 -164.28 -126.34 REMARK 500 2 ALA B 72 19.57 -143.78 REMARK 500 2 ASP B 82 7.36 57.71 REMARK 500 2 LEU B 111 -168.31 -125.44 REMARK 500 3 SER B 44 16.41 53.48 REMARK 500 3 SER B 65 175.12 -53.09 REMARK 500 3 ALA B 72 22.24 -142.28 REMARK 500 3 ASP B 82 10.97 57.06 REMARK 500 3 LEU B 111 -167.70 -121.59 REMARK 500 4 ARG B 56 80.33 -152.41 REMARK 500 4 SER B 65 174.74 -52.88 REMARK 500 4 ASP B 82 11.15 56.25 REMARK 500 4 LEU B 111 -164.22 -122.66 REMARK 500 5 ASN B 53 8.00 -68.17 REMARK 500 5 SER B 65 175.38 -53.82 REMARK 500 5 ALA B 72 19.99 -142.55 REMARK 500 5 ASP B 82 8.44 57.19 REMARK 500 5 ASN B 110 19.10 57.92 REMARK 500 6 ARG B 56 79.63 -155.53 REMARK 500 6 SER B 65 174.61 -51.87 REMARK 500 6 ALA B 72 15.44 -146.34 REMARK 500 6 ASN B 110 19.40 57.65 REMARK 500 7 ARG B 56 78.21 -153.65 REMARK 500 7 SER B 65 172.05 -54.35 REMARK 500 7 SER B 70 -0.36 63.72 REMARK 500 7 ALA B 72 20.19 47.92 REMARK 500 7 ASP B 82 8.94 57.10 REMARK 500 7 LEU B 111 -164.94 -122.30 REMARK 500 8 ARG B 56 81.95 -153.81 REMARK 500 8 SER B 65 170.62 -54.53 REMARK 500 8 ALA B 72 16.84 -141.68 REMARK 500 8 VAL B 81 -133.98 -77.16 REMARK 500 8 ASP B 82 -5.37 -49.79 REMARK 500 8 LEU B 111 -167.34 -127.19 REMARK 500 9 ARG B 56 86.87 -165.91 REMARK 500 9 SER B 65 173.79 -52.74 REMARK 500 9 ALA B 72 19.53 -141.73 REMARK 500 9 ASP B 82 11.29 56.21 REMARK 500 9 THR B 107 -62.93 -101.45 REMARK 500 9 ASN B 110 18.96 58.84 REMARK 500 9 LEU B 111 -162.78 -119.03 REMARK 500 10 ARG B 56 79.48 -157.46 REMARK 500 10 SER B 65 173.93 -52.14 REMARK 500 10 SER B 70 -1.99 78.75 REMARK 500 10 ALA B 72 13.87 -140.30 REMARK 500 10 ASP B 82 11.66 57.00 REMARK 500 REMARK 500 THIS ENTRY HAS 107 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2L2J RELATED DB: PDB DBREF 2L2K B 43 113 UNP Q3UHM7 Q3UHM7_MOUSE 231 301 DBREF 2L2K A 1 42 PDB 2L2K 2L2K 1 42 SEQRES 1 B 71 PRO SER GLY LYS ASN PRO VAL MET ILE LEU ASN GLU LEU SEQRES 2 B 71 ARG PRO GLY LEU LYS TYR ASP PHE LEU SER GLU SER GLY SEQRES 3 B 71 GLU SER HIS ALA LYS SER PHE VAL MET SER VAL VAL VAL SEQRES 4 B 71 ASP GLY GLN PHE PHE GLU GLY SER GLY ARG ASN LYS LYS SEQRES 5 B 71 LEU ALA LYS ALA ARG ALA ALA GLN SER ALA LEU ALA THR SEQRES 6 B 71 VAL PHE ASN LEU HIS LEU SEQRES 1 A 42 G G U A A G G U G G G U G SEQRES 2 A 42 G A A U C C U U C G G G A SEQRES 3 A 42 U C C C A C C U A C C C U SEQRES 4 A 42 G C C HELIX 1 1 ASN B 47 ARG B 56 1 10 HELIX 2 2 ASN B 92 PHE B 109 1 18 SHEET 1 A 3 LYS B 60 SER B 67 0 SHEET 2 A 3 SER B 74 VAL B 81 -1 O VAL B 76 N LEU B 64 SHEET 3 A 3 GLN B 84 GLY B 90 -1 O GLY B 90 N PHE B 75 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