HEADER RNA 02-AUG-23 8TNS TITLE SOLUTION STRUCTURE OF POLY(UG) RNA (GU)12 G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'- COMPND 3 R(*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP*GP*UP* COMPND 4 GP*U)-3'); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 4 ORGANISM_TAXID: 6239 KEYWDS G-QUADRUPLEX, P(UG)-FOLD, RNA EXPDTA SOLUTION NMR; SOLUTION SCATTERING NUMMDL 20 AUTHOR C.A.ESCOBAR,R.PETERSEN,S.E.BUTCHER REVDAT 3 15-MAY-24 8TNS 1 REMARK REVDAT 2 22-NOV-23 8TNS 1 JRNL REVDAT 1 15-NOV-23 8TNS 0 JRNL AUTH C.A.ESCOBAR,R.J.PETERSEN,M.TONELLI,L.FAN, JRNL AUTH 2 K.A.HENZLER-WILDMAN,S.E.BUTCHER JRNL TITL SOLUTION STRUCTURE OF POLY(UG) RNA. JRNL REF J.MOL.BIOL. V. 435 68340 2023 JRNL REFN ESSN 1089-8638 JRNL PMID 37924862 JRNL DOI 10.1016/J.JMB.2023.168340 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SAXS AND RDC WERE USED DURING REMARK 3 REFINEMENT REMARK 4 REMARK 4 8TNS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276186. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293; 276 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : 100; 100 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM (GU)12, 50 MM HEPES, 150 REMARK 210 MM POTASSIUM CHLORIDE, 20 UM DSS, REMARK 210 10 % [U-2H] D2O, 90 % H2O, 90% REMARK 210 H2O/10% D2O; 400 UM (GU)12, 50 REMARK 210 MM HEPES, 150 MM POTASSIUM REMARK 210 CHLORIDE, 20 UM DSS, 100 % [U-2H] REMARK 210 D2O, 100% D2O; 350 UM [U-13C; U- REMARK 210 15N]-GUA (GU)12, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 20 UM DSS, 10 % [U-2H] REMARK 210 D2O, 90 % H2O, 90% H2O/10% D2O; REMARK 210 350 UM [U-13C; U-15N]-GUA (GU)12, REMARK 210 20 MM POTASSIUM PHOSPHATE, 100 REMARK 210 MM POTASSIUM CHLORIDE, 20 UM DSS, REMARK 210 100 % [U-2H] D2O, 100% D2O; 200 REMARK 210 UM [U-13C; U-15N]-URA (GU)12, 20 REMARK 210 MM POTASSIUM PHOSPHATE, 100 MM REMARK 210 POTASSIUM CHLORIDE, 20 UM DSS, REMARK 210 10 % [U-2H] D2O, 90 % H2O, 90% REMARK 210 H2O/10% D2O; 200 UM [U-13C; U- REMARK 210 15N]-URA (GU)12, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 20 UM DSS, 100 % [U-2H] REMARK 210 D2O, 100% D2O; 500 UM (GU)11.5, REMARK 210 20 MM POTASSIUM PHOSPHATE, 100 REMARK 210 MM POTASSIUM CHLORIDE, 20 UM DSS, REMARK 210 100 % [U-2H] D2O, 100% D2O; 350 REMARK 210 UM (GU)12-DG1, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 20 UM DSS, 100 % [U-2H] REMARK 210 D2O, 100% D2O; 770 UM (GU)12- REMARK 210 DU2, 20 MM POTASSIUM PHOSPHATE, REMARK 210 100 MM POTASSIUM CHLORIDE, 20 UM REMARK 210 DSS, 100 % [U-2H] D2O, 100% D2O; REMARK 210 380 UM (GU)12-DG3, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 100 MM REMARK 210 POTASSIUM CHLORIDE, 20 UM DSS, REMARK 210 100 % [U-2H] D2O, 100% D2O; 270 REMARK 210 UM (GU)12-DU4, 20 MM POTASSIUM REMARK 210 PHOSPHATE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 20 UM DSS, 100 % [U-2H] REMARK 210 D2O, 100% D2O; 190 UM (GU)12- REMARK 210 DG5, 20 MM POTASSIUM PHOSPHATE, REMARK 210 100 MM POTASSIUM CHLORIDE, 20 UM REMARK 210 DSS, 100 % [U-2H] D2O, 100% D2O; REMARK 210 210 UM (GU)12-DU6, 20 MM REMARK 210 POTASSIUM PHOSPHATE, 100 MM REMARK 210 POTASSIUM CHLORIDE, 20 UM DSS, REMARK 210 100 % [U-2H] D2O, 100% D2O; 120 REMARK 210 UM [U-13C; U-15N]-GUA (GU)12, 21 REMARK 210 MM POTASSIUM PHOSPHATE, 60 MM REMARK 210 POTASSIUM CHLORIDE, 0.02 % REMARK 210 SODIUM AZIDE, 0.8 MM MAGNESIUM REMARK 210 CHLORIDE, 20 MG/ML PF1 PHAGE, 50 REMARK 210 % H2O, 50 % [U-2H] D2O, 50% H2O/ REMARK 210 50% D2O; 70 UM [U-13C; U-15N]- REMARK 210 URA (GU)12, 21 MM POTASSIUM REMARK 210 PHOSPHATE, 60 MM POTASSIUM REMARK 210 CHLORIDE, 0.02 UM SODIUM AZIDE, REMARK 210 0.8 UM MAGNESIUM CHLORIDE, 20 UM REMARK 210 PF1 PHAGE, 50 % H2O, 50 % [U-2H] REMARK 210 D2O, 50% H2O/50% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H; 1D 31P; 3D H,H,C NOESY REMARK 210 -1H,13C-HSQC SENSITIVITY- REMARK 210 ENHANCED; 3D H,H,C NOESY-1H,13C- REMARK 210 HSQC SENSITIVITY-ENHANCED CC REMARK 210 DECOUPLED; 2D H,H NOESY-1H,15N- REMARK 210 HSQC; 2D H,N HCN BEST; 2D 1H-13C REMARK 210 HSQC SENSITIVITY-ENHANCED CC REMARK 210 DECOUPLED (H1'-C1' H5-C5); 2D 1H- REMARK 210 15N HSQC LONG-RANGE; 2D 1H-13C REMARK 210 HSQC SENSITIVITY-ENHANCED CC REMARK 210 DECOUPLED (H6-C6); 2D 1H-15N REMARK 210 HSQC BEST; 3D H,H,C 13C-FILTERED REMARK 210 NOESY-1H,13C-HSQC SENSITIVITY- REMARK 210 ENHANCED CC DECOUPLED; 3D HCCH- REMARK 210 TOCSY; 3D HCCH-COSY; 2D 1H-13C REMARK 210 HSQC CONSTANT-TIME; 3D HCP REMARK 210 SENSITIVITY-ENHANCED; 3D H,H,C REMARK 210 NOESY-1H,13C-HSQC SENSITIVITY- REMARK 210 ENHANCED (NOES TO RIBOSE); 3D H, REMARK 210 H,C NOESY-1H,13C-HSQC REMARK 210 SENSITIVITY-ENHANCED (NOES TO H8- REMARK 210 C8); 2D 1H-15N HSQC LONG-RANGE REMARK 210 (H8-N9); 3D H,N,N NOESY-1H,15N- REMARK 210 HSQC; 3D H,H,C 13C-FILTERED REMARK 210 NOESY-1H,13C-HSQC SENSITIVITY- REMARK 210 ENHANCED (NOES TO UNLABELED H8- REMARK 210 C8); 3D H,H,C 13C-FILTERED NOESY- REMARK 210 1H,13C-HSQC SENSITIVITY-ENHANCED REMARK 210 (NOES TO UNLABELED RIBOSE); 2D REMARK 210 1H-1H NOESY (200 MS MIX. TIME); REMARK 210 2D 1H-1H NOESY (350 MS MIX. TIME) REMARK 210 ; 2D 1H-1H TOCSY; 2D 1H-15N HSQC REMARK 210 LONG-RANGE (H8-N7); 2D 13C-15N REMARK 210 CON (C2-N1); 2D 13C-15N CON (C2- REMARK 210 N3); 2D 1H-13C HN(CA)CO (H3-C2); REMARK 210 2D ARTSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD; VNMRS DD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ 4.2 REVISION A, TOPSPIN REMARK 210 3.5, MESTRELAB (MNOVA / REMARK 210 MESTRENOVA / MESTREC) 14.3.1- REMARK 210 31739, NMRFAM-SPARKY 1.470, REMARK 210 NMRPIPE, X-PLOR NIH REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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 265 REMARK 265 EXPERIMENTAL DETAILS REMARK 265 REMARK 265 EXPERIMENT TYPE : SMALL ANGLE X-RAY SCATTERING REMARK 265 DATA ACQUISITION REMARK 265 RADIATION/NEUTRON SOURCE : ADVANCE PHOTON SOURCE REMARK 265 SYNCHROTRON (Y/N) : Y REMARK 265 BEAMLINE TYPE : APS REMARK 265 BEAMLINE INSTRUMENT : 12-ID-B REMARK 265 DETECTOR TYPE : PILATUS 2M AND REMARK 265 PILATUS 300K REMARK 265 DETECTOR MANUFACTURER DETAILS : NULL REMARK 265 TEMPERATURE (KELVIN) : 295 REMARK 265 PH : 7.0 REMARK 265 NUMBER OF TIME FRAMES USED : 60 REMARK 265 PROTEIN CONCENTRATION RANGE (MG/ML) : 0.26-1.6 REMARK 265 SAMPLE BUFFER : HEPES REMARK 265 DATA REDUCTION SOFTWARE : IN-HOUSE SOFTWARE REMARK 265 GUINIER MEAN RADIUS OF GYRATION (NM) : 1.3 REMARK 265 SIGMA MEAN RADIUS OF GYRATION : 0.007 REMARK 265 R(XS-1) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-1) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 R(XS-2) MEAN CROSS SECTIONAL RADII (NM) : NULL REMARK 265 R(XS-2) SIGMA MEAN CROSS SECTIONAL RADII : NULL REMARK 265 P(R) PROTEIN LENGTH (NM) : 4.7 REMARK 265 REMARK 265 DATA ANALYSIS AND MODEL FITTING: REMARK 265 METHOD USED TO DETERMINE THE STRUCTURE: HIGH TEMPERATURE DYNAMICS REMARK 265 AT 3000 K, FOLLOWED BY REMARK 265 SUMULATED ANNEALING FROM REMARK 265 3000 K TO 25 K AND A REMARK 265 FINAL ENERGY MINIMIZATION REMARK 265 STEP. REMARK 265 SOFTWARE USED : X-PLOR_NIH REMARK 265 SOFTWARE AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA, CLORE REMARK 265 STARTING MODEL : NULL REMARK 265 REMARK 265 CONFORMERS, NUMBER CALCULATED : 100 REMARK 265 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 265 CONFORMERS, SELECTION CRITERIA : LEAST RESTRAINT VIOLATIONS REMARK 265 REMARK 265 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 265 REMARK 265 OTHER DETAILS: STARTING MODEL WAS BEST MODEL OBTAINED AFTER REMARK 265 CALCULATIONS WITHOUT RDC AND SCATTERING DATA. 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 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 1 U A 8 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 10 U A 14 C3' - O3' - P ANGL. DEV. = 8.9 DEGREES REMARK 500 15 U A 20 C3' - O3' - P ANGL. DEV. = 9.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 G A 17 0.06 SIDE CHAIN REMARK 500 2 G A 11 0.05 SIDE CHAIN REMARK 500 6 G A 11 0.05 SIDE CHAIN REMARK 500 11 G A 11 0.05 SIDE CHAIN REMARK 500 12 G A 11 0.05 SIDE CHAIN REMARK 500 19 G A 11 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 52045 RELATED DB: BMRB REMARK 900 RELATED ID: SASDSW7 RELATED DB: SASBDB DBREF 8TNS A 1 24 PDB 8TNS 8TNS 1 24 SEQRES 1 A 24 G U G U G U G U G U G U G SEQRES 2 A 24 U G U G U G U G U G U 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