HEADER RNA 24-NOV-21 7SXP TITLE G-QUADRUPLEX STRUCTURE FORMED IN THE NRAS MRNA WITH A G8U SUBSTITUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NRAS MRNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, NRAS, RNA EXPDTA X-RAY DIFFRACTION AUTHOR M.T.BANCO,A.R.FERRE-D'AMARE REVDAT 2 05-JUL-23 7SXP 1 JRNL REVDAT 1 31-MAY-23 7SXP 0 JRNL AUTH S.BALARATNAM,Z.R.TORREY,D.R.CALABRESE,M.T.BANCO,K.YAZDANI, JRNL AUTH 2 X.LIANG,C.R.FULLENKAMP,S.SESHADRI,R.J.HOLEWINSKI, JRNL AUTH 3 T.ANDRESSON,A.R.FERRE-D'AMARE,D.INCARNATO, JRNL AUTH 4 J.S.SCHNEEKLOTH JR. JRNL TITL INVESTIGATING THE NRAS 5' UTR AS A TARGET FOR SMALL JRNL TITL 2 MOLECULES. JRNL REF CELL CHEM BIOL V. 30 643 2023 JRNL REFN ESSN 2451-9456 JRNL PMID 37257453 JRNL DOI 10.1016/J.CHEMBIOL.2023.05.004 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487+SVN 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 1331 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.580 REMARK 3 FREE R VALUE TEST SET COUNT : 61 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 31.5300 - 2.9000 0.98 1270 61 0.2408 0.2772 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.715 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 88.13 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 83.24 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 : 0.003 468 REMARK 3 ANGLE : 0.619 732 REMARK 3 CHIRALITY : 0.046 96 REMARK 3 PLANARITY : 0.007 17 REMARK 3 DIHEDRAL : 19.323 223 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 7SXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-21. REMARK 100 THE DEPOSITION ID IS D_1000261103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.104 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 31.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 17.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.32 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 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 : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.19.2_4158 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 - 25 % PEG 3350, 80 MM SODIUM REMARK 280 CHLORIDE AND 100 MM BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 23.36767 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 46.73533 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 46.73533 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 23.36767 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 K K A 101 LIES ON A SPECIAL POSITION. 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 8 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 1 O5' C5' C4' O4' C3' C2' O2' REMARK 470 U A 1 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U A 1 C5 C6 REMARK 470 A A 7 C5' C4' O4' C3' O3' C2' O2' REMARK 470 A A 7 C1' N9 C8 N7 C5 C6 N6 REMARK 470 A A 7 N1 C2 N3 C4 REMARK 470 U A 16 C2 O2 N3 C4 O4 C5 C6 REMARK 470 U A 18 C2 O2 N3 C4 O4 C5 C6 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 K A 101 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 4 O6 REMARK 620 2 G A 4 O6 0.0 REMARK 620 3 G A 9 O6 63.4 63.4 REMARK 620 4 G A 9 O6 63.4 63.4 0.0 REMARK 620 5 G A 13 O6 103.3 103.3 79.7 79.7 REMARK 620 6 G A 13 O6 103.3 103.3 79.7 79.7 0.0 REMARK 620 7 G A 19 O6 64.1 64.1 106.5 106.5 66.7 66.7 REMARK 620 8 G A 19 O6 64.1 64.1 106.5 106.5 66.7 66.7 0.0 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 102 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 4 O6 REMARK 620 2 G A 5 O6 73.5 REMARK 620 3 G A 9 O6 70.1 87.2 REMARK 620 4 G A 10 O6 135.6 70.7 82.7 REMARK 620 5 G A 13 O6 111.7 160.0 77.1 94.8 REMARK 620 6 G A 14 O6 147.2 105.3 142.5 69.0 81.0 REMARK 620 7 G A 19 O6 70.2 133.4 106.4 153.4 64.2 90.6 REMARK 620 8 G A 20 O6 80.7 67.5 145.9 108.0 131.8 69.2 78.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 103 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 5 O6 REMARK 620 2 G A 6 O6 76.0 REMARK 620 3 G A 10 O6 70.5 95.7 REMARK 620 4 G A 11 O6 126.1 67.6 75.0 REMARK 620 5 G A 14 O6 98.0 163.2 67.6 105.5 REMARK 620 6 G A 15 O6 146.7 128.7 120.4 86.7 63.8 REMARK 620 7 G A 20 O6 59.9 125.5 98.0 166.2 60.7 86.8 REMARK 620 8 G A 21 O6 87.7 86.1 156.9 126.2 109.5 74.2 63.2 REMARK 620 N 1 2 3 4 5 6 7 DBREF 7SXP A 1 22 PDB 7SXP 7SXP 1 22 SEQRES 1 A 22 U G U G G G A U G G G C G SEQRES 2 A 22 G G U C U G G G A HET K A 101 1 HET K A 102 1 HET K A 103 1 HET CAD A 104 5 HET CAD A 105 5 HETNAM K POTASSIUM ION HETNAM CAD CACODYLIC ACID HETSYN CAD HYDROXYDIMETHYLARSINE OXIDE FORMUL 2 K 3(K 1+) FORMUL 5 CAD 2(C2 H7 AS O2) LINK O6 G A 4 K K A 101 1555 1555 3.10 LINK O6 G A 4 K K A 101 1555 4555 3.10 LINK O6 G A 4 K K A 102 1555 1555 2.65 LINK O6 G A 5 K K A 102 1555 1555 2.74 LINK O6 G A 5 K K A 103 1555 1555 2.84 LINK O6 G A 6 K K A 103 1555 1555 2.71 LINK O6 G A 9 K K A 101 1555 1555 2.72 LINK O6 G A 9 K K A 101 1555 4555 2.72 LINK O6 G A 9 K K A 102 1555 1555 2.71 LINK O6 G A 10 K K A 102 1555 1555 2.78 LINK O6 G A 10 K K A 103 1555 1555 2.69 LINK O6 G A 11 K K A 103 1555 1555 2.73 LINK O6 G A 13 K K A 101 1555 1555 2.57 LINK O6 G A 13 K K A 101 1555 4555 2.57 LINK O6 G A 13 K K A 102 1555 1555 2.74 LINK O6 G A 14 K K A 102 1555 1555 2.75 LINK O6 G A 14 K K A 103 1555 1555 2.94 LINK O6 G A 15 K K A 103 1555 1555 2.72 LINK O6 G A 19 K K A 101 1555 1555 2.75 LINK O6 G A 19 K K A 101 1555 4555 2.75 LINK O6 G A 19 K K A 102 1555 1555 2.77 LINK O6 G A 20 K K A 102 1555 1555 2.70 LINK O6 G A 20 K K A 103 1555 1555 3.18 LINK O6 G A 21 K K A 103 1555 1555 2.62 CRYST1 36.402 36.402 70.103 90.00 90.00 120.00 P 31 2 1 6 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 0.027471 0.015860 0.000000 0.00000 SCALE2 0.000000 0.031721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014265 0.00000