HEADER DNA-RNA HYBRID 28-MAY-21 7OOO TITLE THE CRYSTAL STRUCTURE OF A DNA:RNA HYBRID DUPLEX SEQUENCE CTTTTCTTTG TITLE 2 CONTAINING AN LNA-AMIDE-LNA MODIFICATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3'); COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*TP*(05A)P*TP*CP*TP*TP*TP*G)-3'); COMPND 7 CHAIN: B, E; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630 KEYWDS AMIDE-LNA, DUPLEX, DNA:RNA, DNA:RNA HYBRID, DNA-RNA HYBRID EXPDTA X-RAY DIFFRACTION AUTHOR C.THORPE,J.HARDWICK,M.A.MCDONOUGH,J.P.HALL,Y.R.BAKER,A.H.EL-SAGHEER, AUTHOR 2 T.BROWN REVDAT 3 07-FEB-24 7OOO 1 REMARK REVDAT 2 15-MAR-23 7OOO 1 COMPND SEQRES HETNAM FORMUL REVDAT 2 2 1 LINK ATOM REVDAT 1 03-AUG-22 7OOO 0 JRNL AUTH Y.R.BAKER,C.THORPE,J.CHEN,L.M.POLLER,L.COX,P.KUMAR,W.F.LIM, JRNL AUTH 2 L.LIE,G.MCCLOREY,S.EPPLE,D.SINGLETON,M.A.MCDONOUGH, JRNL AUTH 3 J.S.HARDWICK,K.E.CHRISTENSEN,M.J.A.WOOD,J.P.HALL, JRNL AUTH 4 A.H.EL-SAGHEER,T.BROWN JRNL TITL AN LNA-AMIDE MODIFICATION THAT ENHANCES THE CELL UPTAKE AND JRNL TITL 2 ACTIVITY OF PHOSPHOROTHIOATE EXON-SKIPPING OLIGONUCLEOTIDES. JRNL REF NAT COMMUN V. 13 4036 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 35821218 JRNL DOI 10.1038/S41467-022-31636-2 REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 4349 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.0800 - 2.5700 0.99 4141 208 0.2326 0.2513 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.000 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 932 REMARK 3 ANGLE : 1.889 1442 REMARK 3 CHIRALITY : 0.095 176 REMARK 3 PLANARITY : 0.005 42 REMARK 3 DIHEDRAL : 14.536 434 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7OOO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1292116128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4398 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 31.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 18.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7NRP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROP SOLUTION 0.5 MM DUPLEX, 40 MM REMARK 280 SODIUM CHLORIDE, 6.0 MM POTASSIUM CHLORIDE, 20 MM SODIUM REMARK 280 CACODYLATE TRIHYDRATE PH 6.0, 15% (V/V) MPD, 6.0 MM SPERMINE REMARK 280 TETRAHYDROCHLORIDE; WELL SOLUTION COMPONENT CONCENTRATIONS ARE REMARK 280 DOUBLE THE CONCENTRATION OF THE DROP SOLUTION AND DO NOT CONTAIN REMARK 280 THE OLIGONUCLEOTIDE DUPLEX, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.64000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 30.32000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 30.32000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 60.64000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E 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 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 05A B 13 O31 REMARK 620 2 05A B 13 O31 0.0 REMARK 620 N 1 DBREF 7OOO A 1 10 PDB 7OOO 7OOO 1 10 DBREF 7OOO B 11 19 PDB 7OOO 7OOO 11 19 DBREF 7OOO D 1 10 PDB 7OOO 7OOO 1 10 DBREF 7OOO E 11 19 PDB 7OOO 7OOO 11 19 SEQRES 1 A 10 C A A A G A A A A G SEQRES 1 B 9 DC DT 05A DT DC DT DT DT DG SEQRES 1 D 10 C A A A G A A A A G SEQRES 1 E 9 DC DT 05A DT DC DT DT DT DG HET 05A B 13 43 HET 05A E 13 43 HET MG B 101 1 HET MG D 101 1 HETNAM 05A [(1R,3R,4R,7S)-3-[5-METHYL-2,4-BIS(OXIDANYLIDENE) HETNAM 2 05A PYRIMIDIN-1-YL]-7-[2-[[(1S,3R,4R,7S)-3-[5-METHYL-2,4- HETNAM 3 05A BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-7-OXIDANYL-2,5- HETNAM 4 05A DIOXABICYCLO[2.2.1]HEPTAN-1-YL]METHYLAMINO]-2- HETNAM 5 05A OXIDANYLIDENE-ETHYL]-2,5-DIOXABICYCLO[2.2.1]HEPTAN-1- HETNAM 6 05A YL]METHYL DIHYDROGEN PHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 05A 2(C24 H30 N5 O14 P) FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *(H2 O) LINK O3' DT B 12 P 05A B 13 1555 1555 1.59 LINK O3' 05A B 13 P DT B 14 1555 1555 1.62 LINK O3' DT E 12 P 05A E 13 1555 1555 1.62 LINK O3' 05A E 13 P DT E 14 1555 1555 1.63 LINK O31 05A B 13 MG MG B 101 1555 1555 2.30 LINK O31 05A B 13 MG MG B 101 1555 6554 2.75 CRYST1 49.150 49.150 90.960 90.00 90.00 120.00 P 32 2 1 12 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 0.020346 0.011747 0.000000 0.00000 SCALE2 0.000000 0.023493 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010994 0.00000