HEADER RNA 02-MAY-23 8SP9 TITLE CRYSTAL STRUCTURE OF COXSACKIEVIRUS B3 (CVB3) CLOVERLEAF RNA WITH TRNA TITLE 2 SCAFFOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA SCAFFOLD,CVB3 CLOVERLEAF RNA; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS, COXSACKIEVIRUS B3; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606, 12072; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CLOVERLEAF, BASE-TRIPLE, PICORNAVIRUS, TRNA-SCAFFOLD, RNA EXPDTA X-RAY DIFFRACTION AUTHOR K.GOTTIPATI,S.C.MCNEME,K.H.CHOI REVDAT 2 20-SEP-23 8SP9 1 JRNL REVDAT 1 09-AUG-23 8SP9 0 JRNL AUTH K.GOTTIPATI,S.C.MCNEME,J.TIPO,M.A.WHITE,K.H.CHOI JRNL TITL STRUCTURAL BASIS FOR CLOVERLEAF RNA-INITIATED VIRAL GENOME JRNL TITL 2 REPLICATION. JRNL REF NUCLEIC ACIDS RES. V. 51 8850 2023 JRNL REFN ESSN 1362-4962 JRNL PMID 37486760 JRNL DOI 10.1093/NAR/GKAD618 REMARK 2 REMARK 2 RESOLUTION. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.790 REMARK 3 COMPLETENESS FOR RANGE (%) : 63.3 REMARK 3 NUMBER OF REFLECTIONS : 7020 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.292 REMARK 3 R VALUE (WORKING SET) : 0.291 REMARK 3 FREE R VALUE : 0.308 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 348 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 44.6900 - 3.6800 0.83 4432 234 0.2794 0.2835 REMARK 3 2 3.6800 - 2.9200 0.43 2240 114 0.3318 0.3945 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) : 0.266 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.658 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 105.0 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 : 0.002 3231 REMARK 3 ANGLE : 0.688 5032 REMARK 3 CHIRALITY : 0.036 680 REMARK 3 PLANARITY : 0.004 136 REMARK 3 DIHEDRAL : 20.865 1626 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 19 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1704 3.8652 31.3695 REMARK 3 T TENSOR REMARK 3 T11: 2.1060 T22: 1.1480 REMARK 3 T33: 0.1595 T12: 0.5155 REMARK 3 T13: -0.2590 T23: -0.0153 REMARK 3 L TENSOR REMARK 3 L11: 1.9582 L22: 1.2701 REMARK 3 L33: 1.8790 L12: 0.6725 REMARK 3 L13: 1.8766 L23: 0.9464 REMARK 3 S TENSOR REMARK 3 S11: 0.0396 S12: -0.4841 S13: 0.2402 REMARK 3 S21: -0.1815 S22: -0.0806 S23: -0.0921 REMARK 3 S31: -0.3239 S32: 0.1136 S33: 0.0649 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 20 THROUGH 42 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.9985 6.3385 -4.5311 REMARK 3 T TENSOR REMARK 3 T11: 1.9321 T22: 1.2682 REMARK 3 T33: 0.4639 T12: 0.2300 REMARK 3 T13: -0.0516 T23: -0.0152 REMARK 3 L TENSOR REMARK 3 L11: 2.1770 L22: 2.1026 REMARK 3 L33: 9.6273 L12: 1.8399 REMARK 3 L13: -3.3958 L23: -2.4063 REMARK 3 S TENSOR REMARK 3 S11: 0.0939 S12: -0.2594 S13: -0.1021 REMARK 3 S21: -0.0414 S22: -0.1449 S23: -0.1020 REMARK 3 S31: 0.3261 S32: 1.3455 S33: 0.0610 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 43 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 42.7346 4.5045 -16.8474 REMARK 3 T TENSOR REMARK 3 T11: 1.1384 T22: 3.0837 REMARK 3 T33: 2.0350 T12: -0.3294 REMARK 3 T13: 0.4899 T23: -0.3058 REMARK 3 L TENSOR REMARK 3 L11: 5.8131 L22: 1.9999 REMARK 3 L33: 1.9996 L12: -8.3371 REMARK 3 L13: -7.8291 L23: 2.0003 REMARK 3 S TENSOR REMARK 3 S11: 0.6372 S12: 0.5033 S13: -0.4524 REMARK 3 S21: -1.6256 S22: -0.0182 S23: -1.5271 REMARK 3 S31: -0.8489 S32: 0.3859 S33: -0.6232 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 60 THROUGH 83 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5306 11.8308 -35.3058 REMARK 3 T TENSOR REMARK 3 T11: 1.8636 T22: 1.0294 REMARK 3 T33: 0.1285 T12: 0.1745 REMARK 3 T13: 0.4580 T23: 0.2758 REMARK 3 L TENSOR REMARK 3 L11: 6.4293 L22: 3.9289 REMARK 3 L33: 7.9675 L12: -1.4323 REMARK 3 L13: -1.0228 L23: -0.4636 REMARK 3 S TENSOR REMARK 3 S11: 0.2726 S12: -0.4626 S13: -0.4490 REMARK 3 S21: -0.4623 S22: -0.0290 S23: -1.1823 REMARK 3 S31: 0.9943 S32: 1.6886 S33: 0.0736 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 84 THROUGH 98 ) REMARK 3 ORIGIN FOR THE GROUP (A): 11.9093 24.2055 -55.0817 REMARK 3 T TENSOR REMARK 3 T11: 1.5665 T22: 1.7932 REMARK 3 T33: 0.2150 T12: 0.1907 REMARK 3 T13: 0.1849 T23: 0.0618 REMARK 3 L TENSOR REMARK 3 L11: 3.5053 L22: 3.9770 REMARK 3 L33: 9.3505 L12: -0.3022 REMARK 3 L13: -0.1920 L23: -2.0865 REMARK 3 S TENSOR REMARK 3 S11: 0.2911 S12: 0.8303 S13: 0.3562 REMARK 3 S21: -1.0881 S22: 0.1632 S23: 0.5486 REMARK 3 S31: -0.8010 S32: -1.5452 S33: -0.4165 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 99 THROUGH 125 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.9281 8.6174 -12.3738 REMARK 3 T TENSOR REMARK 3 T11: 1.6249 T22: 0.9610 REMARK 3 T33: -0.0935 T12: 0.0371 REMARK 3 T13: 0.3572 T23: 0.0818 REMARK 3 L TENSOR REMARK 3 L11: 0.2292 L22: 0.6994 REMARK 3 L33: 4.2938 L12: 0.0846 REMARK 3 L13: -0.0637 L23: -1.3751 REMARK 3 S TENSOR REMARK 3 S11: 0.2015 S12: -0.4440 S13: -0.2456 REMARK 3 S21: 0.1338 S22: 0.2113 S23: 0.0958 REMARK 3 S31: 0.4936 S32: 0.0220 S33: -0.1721 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 126 THROUGH 151 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7522 -2.3696 39.0806 REMARK 3 T TENSOR REMARK 3 T11: 0.7840 T22: 0.9616 REMARK 3 T33: 0.0766 T12: -0.2499 REMARK 3 T13: -0.1971 T23: -0.0290 REMARK 3 L TENSOR REMARK 3 L11: 1.4369 L22: 1.3511 REMARK 3 L33: 4.0504 L12: -0.7653 REMARK 3 L13: -0.5811 L23: 0.5535 REMARK 3 S TENSOR REMARK 3 S11: 0.4716 S12: 0.1352 S13: 0.3388 REMARK 3 S21: -0.2035 S22: 0.2198 S23: -0.4647 REMARK 3 S31: -0.8424 S32: 0.7085 S33: -0.4633 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 8SP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1000274205. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9250 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.3 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.97 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS, PH 6.5, 48% REMARK 280 POLYPROPYLENE GLYCOL (PPG)-P400, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 14.17950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 G C 44 REMARK 465 G C 45 REMARK 465 G C 46 REMARK 465 U C 47 REMARK 465 U C 48 REMARK 465 G C 49 REMARK 465 A C 50 REMARK 465 U C 51 REMARK 465 C C 52 REMARK 465 C C 53 REMARK 465 C C 54 REMARK 465 A C 55 REMARK 465 C C 56 REMARK 465 C C 57 REMARK 465 C C 58 REMARK 465 C C 152 REMARK 465 A C 153 DBREF 8SP9 C 1 26 GB U00939.1 U00939.1 1 26 DBREF1 8SP9 C 31 116 GB NC_038307.1 DBREF2 8SP9 C NC_038307.1 2 87 DBREF 8SP9 C 121 153 GB U00939.1 U00939.1 44 76 SEQADV 8SP9 G C 27 GB U00939.1 LINKER SEQADV 8SP9 C C 28 GB U00939.1 LINKER SEQADV 8SP9 G C 29 GB U00939.1 LINKER SEQADV 8SP9 G C 30 GB U00939.1 LINKER SEQADV 8SP9 C C 117 GB NC_038307 LINKER SEQADV 8SP9 C C 118 GB NC_038307 LINKER SEQADV 8SP9 G C 119 GB NC_038307 LINKER SEQADV 8SP9 C C 120 GB NC_038307 LINKER SEQRES 1 C 153 G C C C G G A U A G C U C SEQRES 2 C 153 A G U C G G U A G A G C A SEQRES 3 C 153 G C G G U A A A A C A G C SEQRES 4 C 153 C U G U G G G U U G A U C SEQRES 5 C 153 C C A C C C A C A G G G C SEQRES 6 C 153 C C A U U G G G C G C U A SEQRES 7 C 153 G C A C U C U G G U A U C SEQRES 8 C 153 A C G G U A C C U U U G U SEQRES 9 C 153 G C G C C U G U U U U A C SEQRES 10 C 153 C G C G G G U C C A G G G SEQRES 11 C 153 U U C A A G U C C C U G U SEQRES 12 C 153 U C G G G C G C C A CRYST1 76.429 28.359 113.111 90.00 92.01 90.00 P 1 21 1 2 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 0.013084 0.000000 0.000460 0.00000 SCALE2 0.000000 0.035262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008846 0.00000