HEADER RNA 27-AUG-25 9WHV TITLE CROSS-STACKING-STABILIZED INTRA-LOCKED RNA G-QUADRUPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*GP*UP*UP*AP*GP*GP*GP*UP*UP*A)-3'); COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS G-QUADRUPLEX, 16-LAYERS, INTERLOCKED, HIGH SERUM STABILITY, RNA EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR C.D.XIAO,L.W.WANG,S.Y.WANG,Y.XU REVDAT 1 15-OCT-25 9WHV 0 JRNL AUTH C.D.XIAO,S.S.SONG,L.YANG,L.W.WANG,R.Q.TIAN,S.Y.WANG,M.H.JIA, JRNL AUTH 2 Y.XU,M.Q.ZHANG,X.G.LIANG,K.L.HU,H.LUO,Y.CHEN,X.X.HU,X.C.SHEN JRNL TITL CROSS-STACKING-STABILIZED INTRA-LOCKED RNA G-QUADRUPLEX JRNL TITL 2 OVERCOMES SERUM INSTABILITY FOR SUSTAINED CANCER TARGETING JRNL REF TO BE PUBLISHED JRNL REFN 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: NULL REMARK 4 REMARK 4 9WHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 29-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1300063035. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 116 REMARK 210 PRESSURE : 0.1 ATM REMARK 210 SAMPLE CONTENTS : 8.2 MM RNA (5' REMARK 210 -R(*GP*UP*UP*AP*GP*GP*GP*UP*UP*A)-3'), 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D 1H-13C HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 10 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 1 G A 1 C5' G A 1 C4' -0.081 REMARK 500 1 G A 1 C3' G A 1 C2' -0.120 REMARK 500 1 G A 1 O4' G A 1 C4' -0.132 REMARK 500 1 G A 1 C1' G A 1 N9 -0.100 REMARK 500 1 G A 1 C2' G A 1 O2' -0.102 REMARK 500 1 G A 1 N1 G A 1 C2 -0.156 REMARK 500 1 G A 1 C2 G A 1 N3 -0.093 REMARK 500 1 G A 1 N3 G A 1 C4 -0.112 REMARK 500 1 G A 1 C4 G A 1 C5 -0.078 REMARK 500 1 G A 1 C5 G A 1 C6 -0.093 REMARK 500 1 G A 1 C6 G A 1 N1 -0.106 REMARK 500 1 G A 1 C5 G A 1 N7 -0.110 REMARK 500 1 G A 1 N7 G A 1 C8 -0.066 REMARK 500 1 G A 1 C8 G A 1 N9 -0.137 REMARK 500 1 G A 1 N9 G A 1 C4 -0.086 REMARK 500 1 G A 1 C2 G A 1 N2 -0.117 REMARK 500 1 G A 1 C6 G A 1 O6 -0.110 REMARK 500 1 U A 2 N1 U A 2 C6 -0.063 REMARK 500 1 U A 2 C5 U A 2 C6 0.063 REMARK 500 1 U A 3 O5' U A 3 C5' -0.056 REMARK 500 1 U A 3 N3 U A 3 C4 -0.110 REMARK 500 1 U A 3 C5 U A 3 C6 0.055 REMARK 500 1 A A 4 P A A 4 OP1 0.125 REMARK 500 1 A A 4 C5 A A 4 N7 -0.050 REMARK 500 1 A A 4 O3' G A 5 P -0.074 REMARK 500 1 G A 5 O4' G A 5 C4' -0.087 REMARK 500 1 G A 5 N1 G A 5 C2 -0.066 REMARK 500 1 G A 5 C4 G A 5 C5 0.048 REMARK 500 1 G A 5 C5 G A 5 N7 0.048 REMARK 500 1 G A 5 N7 G A 5 C8 0.040 REMARK 500 1 G A 5 O3' G A 6 P -0.078 REMARK 500 1 G A 6 P G A 6 OP2 0.122 REMARK 500 1 G A 6 C5' G A 6 C4' 0.080 REMARK 500 1 G A 6 N3 G A 6 C4 0.049 REMARK 500 1 G A 6 C8 G A 6 N9 -0.043 REMARK 500 1 G A 7 P G A 7 O5' -0.093 REMARK 500 1 G A 7 O5' G A 7 C5' -0.093 REMARK 500 1 G A 7 C5' G A 7 C4' -0.081 REMARK 500 1 G A 7 C3' G A 7 C2' -0.103 REMARK 500 1 G A 7 O4' G A 7 C4' -0.138 REMARK 500 1 G A 7 C1' G A 7 N9 -0.107 REMARK 500 1 G A 7 N1 G A 7 C2 -0.151 REMARK 500 1 G A 7 C2 G A 7 N3 -0.098 REMARK 500 1 G A 7 N3 G A 7 C4 -0.108 REMARK 500 1 G A 7 C4 G A 7 C5 -0.076 REMARK 500 1 G A 7 C5 G A 7 C6 -0.098 REMARK 500 1 G A 7 C6 G A 7 N1 -0.117 REMARK 500 1 G A 7 C5 G A 7 N7 -0.111 REMARK 500 1 G A 7 N7 G A 7 C8 -0.056 REMARK 500 1 G A 7 C8 G A 7 N9 -0.134 REMARK 500 REMARK 500 THIS ENTRY HAS 7695 BOND DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 G A 1 C2 - N3 - C4 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 G A 1 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 G A 1 C4 - C5 - N7 ANGL. DEV. = -2.5 DEGREES REMARK 500 1 U A 2 O3' - P - O5' ANGL. DEV. = 11.6 DEGREES REMARK 500 1 U A 2 OP1 - P - OP2 ANGL. DEV. = -11.9 DEGREES REMARK 500 1 U A 2 C4 - C5 - C6 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 U A 2 C6 - N1 - C1' ANGL. DEV. = -9.7 DEGREES REMARK 500 1 U A 3 O3' - P - O5' ANGL. DEV. = 12.0 DEGREES REMARK 500 1 U A 3 OP1 - P - OP2 ANGL. DEV. = -12.4 DEGREES REMARK 500 1 U A 3 C1' - O4' - C4' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 U A 3 O4' - C1' - C2' ANGL. DEV. = -9.8 DEGREES REMARK 500 1 U A 3 O4' - C1' - N1 ANGL. DEV. = 6.3 DEGREES REMARK 500 1 A A 4 O3' - P - O5' ANGL. DEV. = 16.9 DEGREES REMARK 500 1 A A 4 OP1 - P - OP2 ANGL. DEV. = -14.9 DEGREES REMARK 500 1 A A 4 N1 - C2 - N3 ANGL. DEV. = -4.1 DEGREES REMARK 500 1 A A 4 C2 - N3 - C4 ANGL. DEV. = 9.1 DEGREES REMARK 500 1 A A 4 N3 - C4 - C5 ANGL. DEV. = -8.3 DEGREES REMARK 500 1 A A 4 C4 - C5 - C6 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A A 4 C4 - C5 - N7 ANGL. DEV. = -3.8 DEGREES REMARK 500 1 A A 4 C8 - N9 - C4 ANGL. DEV. = -3.5 DEGREES REMARK 500 1 A A 4 N9 - C4 - C5 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 G A 5 OP1 - P - OP2 ANGL. DEV. = -12.4 DEGREES REMARK 500 1 G A 5 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 G A 5 C2 - N3 - C4 ANGL. DEV. = 7.5 DEGREES REMARK 500 1 G A 5 N3 - C4 - C5 ANGL. DEV. = -9.7 DEGREES REMARK 500 1 G A 5 C4 - C5 - N7 ANGL. DEV. = -6.8 DEGREES REMARK 500 1 G A 5 N7 - C8 - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G A 5 C8 - N9 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 G A 5 N9 - C4 - C5 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 G A 6 C4' - C3' - C2' ANGL. DEV. = 6.0 DEGREES REMARK 500 1 G A 6 C3' - C2' - C1' ANGL. DEV. = -5.8 DEGREES REMARK 500 1 G A 6 N3 - C4 - C5 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 G A 6 C4 - C5 - N7 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 G A 6 N3 - C4 - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G A 6 N1 - C2 - N2 ANGL. DEV. = 7.9 DEGREES REMARK 500 1 G A 6 N3 - C2 - N2 ANGL. DEV. = -8.4 DEGREES REMARK 500 1 G A 6 N1 - C6 - O6 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 G A 6 C5 - C6 - O6 ANGL. DEV. = -5.3 DEGREES REMARK 500 1 G A 6 C8 - N9 - C1' ANGL. DEV. = 8.9 DEGREES REMARK 500 1 G A 7 O3' - P - O5' ANGL. DEV. = 15.8 DEGREES REMARK 500 1 G A 7 OP1 - P - OP2 ANGL. DEV. = -9.6 DEGREES REMARK 500 1 G A 7 C1' - O4' - C4' ANGL. DEV. = -4.6 DEGREES REMARK 500 1 G A 7 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 G A 7 C2 - N3 - C4 ANGL. DEV. = 4.5 DEGREES REMARK 500 1 G A 7 N3 - C4 - C5 ANGL. DEV. = -5.2 DEGREES REMARK 500 1 G A 7 C3' - O3' - P ANGL. DEV. = 7.5 DEGREES REMARK 500 1 U A 8 O3' - P - O5' ANGL. DEV. = 13.5 DEGREES REMARK 500 1 U A 8 OP1 - P - OP2 ANGL. DEV. = -12.7 DEGREES REMARK 500 1 U A 8 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 U A 8 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 5175 ANGLE DEVIATIONS. 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 B 1 0.07 SIDE CHAIN REMARK 500 1 G D 5 0.07 SIDE CHAIN REMARK 500 1 G D 6 0.07 SIDE CHAIN REMARK 500 1 G E 5 0.09 SIDE CHAIN REMARK 500 1 U G 3 0.10 SIDE CHAIN REMARK 500 1 G H 5 0.06 SIDE CHAIN REMARK 500 2 A A 4 0.07 SIDE CHAIN REMARK 500 2 G B 1 0.07 SIDE CHAIN REMARK 500 2 U C 2 0.06 SIDE CHAIN REMARK 500 2 G C 6 0.06 SIDE CHAIN REMARK 500 2 G E 5 0.10 SIDE CHAIN REMARK 500 2 A G 4 0.06 SIDE CHAIN REMARK 500 2 G G 6 0.09 SIDE CHAIN REMARK 500 2 U H 3 0.06 SIDE CHAIN REMARK 500 3 G B 1 0.07 SIDE CHAIN REMARK 500 3 G D 5 0.06 SIDE CHAIN REMARK 500 3 G E 5 0.08 SIDE CHAIN REMARK 500 3 G E 6 0.07 SIDE CHAIN REMARK 500 3 U F 2 0.07 SIDE CHAIN REMARK 500 4 U A 2 0.07 SIDE CHAIN REMARK 500 4 A A 4 0.06 SIDE CHAIN REMARK 500 4 G B 1 0.07 SIDE CHAIN REMARK 500 4 U D 3 0.07 SIDE CHAIN REMARK 500 4 G D 5 0.07 SIDE CHAIN REMARK 500 4 G D 6 0.06 SIDE CHAIN REMARK 500 4 G E 5 0.10 SIDE CHAIN REMARK 500 4 U F 3 0.10 SIDE CHAIN REMARK 500 4 G F 6 0.07 SIDE CHAIN REMARK 500 4 G H 6 0.06 SIDE CHAIN REMARK 500 5 U A 2 0.07 SIDE CHAIN REMARK 500 5 A A 4 0.07 SIDE CHAIN REMARK 500 5 G B 1 0.07 SIDE CHAIN REMARK 500 5 G E 5 0.06 SIDE CHAIN REMARK 500 5 G F 6 0.08 SIDE CHAIN REMARK 500 5 G G 6 0.09 SIDE CHAIN REMARK 500 5 U H 2 0.07 SIDE CHAIN REMARK 500 5 G H 6 0.10 SIDE CHAIN REMARK 500 6 G A 5 0.09 SIDE CHAIN REMARK 500 6 G B 1 0.07 SIDE CHAIN REMARK 500 6 G B 6 0.08 SIDE CHAIN REMARK 500 6 G C 5 0.07 SIDE CHAIN REMARK 500 6 G D 6 0.07 SIDE CHAIN REMARK 500 6 G E 5 0.06 SIDE CHAIN REMARK 500 6 U F 2 0.07 SIDE CHAIN REMARK 500 6 G F 5 0.07 SIDE CHAIN REMARK 500 6 G F 6 0.05 SIDE CHAIN REMARK 500 7 G B 1 0.07 SIDE CHAIN REMARK 500 7 U B 3 0.07 SIDE CHAIN REMARK 500 7 G C 5 0.06 SIDE CHAIN REMARK 500 7 U E 2 0.07 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 76 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36780 RELATED DB: BMRB REMARK 900 CROSS-STACKING-STABILIZED INTRA-LOCKED RNA G-QUADRUPLEX; EIGHT REMARK 900 IDENTICAL RNA STRANDS (A THROUGH H) ASSEMBLE INTO STACKED G- REMARK 900 QUADRUPLETS. CONSEQUENTLY, THE CHEMICAL SHIFTS FOR EACH STRAND ARE REMARK 900 IDENTICAL. THE CHEMICAL SHIFT DATA WE PROVIDE BASED ON STRAND H REMARK 900 FULLY REPRESENTS THE NMR IDENTIFICATION FOR THE ENTIRE ASSEMBLY. DBREF 9WHV A 1 10 PDB 9WHV 9WHV 1 10 DBREF 9WHV B 1 10 PDB 9WHV 9WHV 1 10 DBREF 9WHV C 1 10 PDB 9WHV 9WHV 1 10 DBREF 9WHV D 1 10 PDB 9WHV 9WHV 1 10 DBREF 9WHV E 1 10 PDB 9WHV 9WHV 1 10 DBREF 9WHV F 1 10 PDB 9WHV 9WHV 1 10 DBREF 9WHV G 1 10 PDB 9WHV 9WHV 1 10 DBREF 9WHV H 1 10 PDB 9WHV 9WHV 1 10 SEQRES 1 A 10 G U U A G G G U U A SEQRES 1 B 10 G U U A G G G U U A SEQRES 1 C 10 G U U A G G G U U A SEQRES 1 D 10 G U U A G G G U U A SEQRES 1 E 10 G U U A G G G U U A SEQRES 1 F 10 G U U A G G G U U A SEQRES 1 G 10 G U U A G G G U U A SEQRES 1 H 10 G U U A G G G U U A 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MASTER 282 0 0 0 0 0 0 6 1704 8 0 8 END