HEADER RNA 20-NOV-23 8V1H TITLE CRYSTAL STRUCTURE OF HUMAN PRE-MASCRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRE-MASCRNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NON-CODING RNAS, CANCER, RNA, MASCRNA EXPDTA X-RAY DIFFRACTION AUTHOR I.SKEPARNIAS,J.ZHANG REVDAT 2 17-JUL-24 8V1H 1 JRNL REVDAT 1 10-JUL-24 8V1H 0 JRNL AUTH I.SKEPARNIAS,C.BOU-NADER,D.G.ANASTASAKIS,L.FAN,Y.X.WANG, JRNL AUTH 2 M.HAFNER,J.ZHANG JRNL TITL STRUCTURAL BASIS OF MALAT1 RNA MATURATION AND MASCRNA JRNL TITL 2 BIOGENESIS. JRNL REF NAT.STRUCT.MOL.BIOL. 2024 JRNL REFN ESSN 1545-9985 JRNL PMID 38956168 JRNL DOI 10.1038/S41594-024-01340-4 REMARK 2 REMARK 2 RESOLUTION. 2.89 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) : 2.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 4832 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.270 REMARK 3 FREE R VALUE TEST SET COUNT : 255 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.300 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 : 0.005 1717 REMARK 3 ANGLE : 1.062 2675 REMARK 3 CHIRALITY : 0.043 360 REMARK 3 PLANARITY : 0.006 72 REMARK 3 DIHEDRAL : 14.008 868 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -0.5873 6.2369 33.2639 REMARK 3 T TENSOR REMARK 3 T11: 0.4735 T22: 0.9174 REMARK 3 T33: 0.7728 T12: -0.2042 REMARK 3 T13: 0.1909 T23: -0.1045 REMARK 3 L TENSOR REMARK 3 L11: 3.7894 L22: 1.3389 REMARK 3 L33: 0.7560 L12: -0.7525 REMARK 3 L13: 0.0495 L23: -0.0587 REMARK 3 S TENSOR REMARK 3 S11: 0.2679 S12: -0.7433 S13: 0.3500 REMARK 3 S21: 0.0023 S22: -0.0918 S23: -0.0150 REMARK 3 S31: -0.0737 S32: 0.1626 S33: -0.2403 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 8V1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1000279347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5028 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 40.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CHLORIDE, 0.1 M LITHIUM REMARK 280 CHLORIDE, 0.01 M MAGNESIUM CHLORIDE HEXAHYDRATE, 0.05 M MES (PH REMARK 280 6.5) AND 35% MPD, PH 7, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 22.49300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.32550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.49300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.32550 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 U A 25 REMARK 465 U A 26 REMARK 465 U A 27 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 U A 13 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U A 13 C6 DBREF 8V1H A -8 66 PDB 8V1H 8V1H -8 66 SEQRES 1 A 75 GTP G C C C G G A C G A U G SEQRES 2 A 75 C U G G U G G U U G G C A SEQRES 3 A 75 C U C C U G G U U U C C A SEQRES 4 A 75 G G A C G G G G U U C A A SEQRES 5 A 75 A U C C C U G C G G C G U SEQRES 6 A 75 C G U C C G G G C C HET GTP A -8 32 HET NA A 101 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM NA SODIUM ION FORMUL 1 GTP C10 H16 N5 O14 P3 FORMUL 2 NA NA 1+ LINK O3' GTP A -8 P G A -7 1555 1555 1.62 CRYST1 44.986 40.651 123.393 90.00 96.99 90.00 C 1 2 1 4 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 0.022229 0.000000 0.002726 0.00000 SCALE2 0.000000 0.024599 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008165 0.00000 HETATM 1 PG GTP A -8 -25.222 9.384 62.730 1.00166.54 P ANISOU 1 PG GTP A -8 15437 30990 16850 -1165 3830 -1875 P HETATM 2 O1G GTP A -8 -23.871 10.048 62.565 1.00145.57 O ANISOU 2 O1G GTP A -8 12847 28331 14133 -1208 3693 -2257 O HETATM 3 O2G GTP A -8 -25.917 9.124 61.414 1.00145.04 O ANISOU 3 O2G GTP A -8 12809 27706 14595 -1234 3872 -1679 O HETATM 4 O3G GTP A -8 -26.111 10.099 63.727 1.00138.59 O ANISOU 4 O3G GTP A -8 11758 27787 13114 -1056 3944 -2114 O HETATM 5 O3B GTP A -8 -24.912 7.922 63.347 1.00162.80 O ANISOU 5 O3B GTP A -8 14918 30809 16130 -1157 3796 -1322 O HETATM 6 PB GTP A -8 -24.329 7.387 64.742 1.00190.45 P ANISOU 6 PB GTP A -8 18298 34932 19131 -1081 3752 -1170 P HETATM 7 O1B GTP A -8 -23.015 8.045 65.031 1.00153.59 O ANISOU 7 O1B GTP A -8 13643 30469 14245 -1086 3616 -1565 O HETATM 8 O2B GTP A -8 -25.422 7.411 65.766 1.00145.62 O ANISOU 8 O2B GTP A -8 12469 29616 13244 -975 3887 -1095 O HETATM 9 O3A GTP A -8 -24.036 5.862 64.360 1.00147.01 O ANISOU 9 O3A GTP A -8 12842 29290 13725 -1139 3701 -561 O HETATM 10 PA GTP A -8 -23.154 5.170 63.218 1.00119.65 P ANISOU 10 PA GTP A -8 9523 25407 10530 -1252 3581 -352 P HETATM 11 O1A GTP A -8 -23.695 5.530 61.874 1.00115.84 O ANISOU 11 O1A GTP A -8 9156 24345 10513 -1327 3615 -455 O HETATM 12 O2A GTP A -8 -21.713 5.460 63.478 1.00147.83 O ANISOU 12 O2A GTP A -8 13117 29189 13863 -1261 3441 -587 O HETATM 13 O5' GTP A -8 -23.463 3.632 63.545 1.00120.87 O ANISOU 13 O5' GTP A -8 9615 25648 10663 -1244 3597 298 O HETATM 14 C5' GTP A -8 -23.134 2.663 62.528 1.00117.53 C ANISOU 14 C5' GTP A -8 9293 24807 10558 -1337 3525 641 C HETATM 15 C4' GTP A -8 -23.648 1.300 62.922 1.00119.34 C ANISOU 15 C4' GTP A -8 9432 25108 10803 -1322 3559 1228 C HETATM 16 O4' GTP A -8 -24.906 1.420 63.641 1.00127.68 O ANISOU 16 O4' GTP A -8 10362 26370 11782 -1251 3709 1296 O HETATM 17 C3' GTP A -8 -23.950 0.371 61.740 1.00116.14 C ANISOU 17 C3' GTP A -8 9107 24159 10862 -1418 3534 1568 C HETATM 18 O3' GTP A -8 -22.798 -0.361 61.334 1.00115.44 O ANISOU 18 O3' GTP A -8 9090 23958 10813 -1468 3393 1753 O HETATM 19 C2' GTP A -8 -25.176 -0.411 62.227 1.00118.80 C ANISOU 19 C2' GTP A -8 9313 24556 11268 -1385 3649 1972 C HETATM 20 O2' GTP A -8 -24.838 -1.448 63.121 1.00121.74 O ANISOU 20 O2' GTP A -8 9582 25256 11417 -1340 3619 2398 O HETATM 21 C1' GTP A -8 -25.915 0.699 62.967 1.00121.31 C ANISOU 21 C1' GTP A -8 9552 25177 11362 -1304 3776 1626 C HETATM 22 N9 GTP A -8 -26.673 1.627 62.122 1.00119.03 N ANISOU 22 N9 GTP A -8 9325 24536 11364 -1336 3845 1289 N HETATM 23 C8 GTP A -8 -26.593 2.996 62.154 1.00118.81 C ANISOU 23 C8 GTP A -8 9329 24580 11234 -1304 3868 758 C HETATM 24 N7 GTP A -8 -27.392 3.589 61.300 1.00116.77 N ANISOU 24 N7 GTP A -8 9112 23949 11306 -1335 3930 571 N HETATM 25 C5 GTP A -8 -28.047 2.542 60.671 1.00115.57 C ANISOU 25 C5 GTP A -8 8953 23472 11487 -1395 3945 993 C HETATM 26 C6 GTP A -8 -29.033 2.572 59.653 1.00113.43 C ANISOU 26 C6 GTP A -8 8700 22750 11648 -1447 3993 1019 C HETATM 27 O6 GTP A -8 -29.536 3.562 59.106 1.00112.14 O ANISOU 27 O6 GTP A -8 8564 22388 11655 -1442 4040 685 O HETATM 28 N1 GTP A -8 -29.430 1.286 59.292 1.00113.06 N ANISOU 28 N1 GTP A -8 8622 22483 11853 -1505 3974 1489 N HETATM 29 C2 GTP A -8 -28.946 0.123 59.837 1.00114.58 C ANISOU 29 C2 GTP A -8 8774 22849 11913 -1509 3920 1897 C HETATM 30 N2 GTP A -8 -29.448 -1.020 59.357 1.00114.13 N ANISOU 30 N2 GTP A -8 8684 22506 12176 -1572 3900 2304 N HETATM 31 N3 GTP A -8 -28.023 0.088 60.801 1.00116.61 N ANISOU 31 N3 GTP A -8 9012 23537 11758 -1453 3880 1900 N HETATM 32 C4 GTP A -8 -27.618 1.326 61.167 1.00116.97 C ANISOU 32 C4 GTP A -8 9086 23818 11539 -1399 3893 1432 C