RNA Structure

Dual Topology: 3_4


Topological Aspects

  • 3 Vertices


  • Eigenvalues
    • 0.0000000000
      2.0000000000
      6.0000000000


    Examples of actual RNAs corresponding to this structure from RNA databases: 176

    PDB_Chain Type Discovery Method
    1A9L_A PRE-TRNA BULGE-HELIX-BULGE MOTIFSOLUTION NMR
    1CQ5_A SRP RNA DOMAIN IVSOLUTION NMR
    1CQL_A SRP DOMAIN IV RNASOLUTION NMR
    1DUL_B 4.5 S RNA DOMAIN IVX-RAY DIFFRACTION
    1DZ5_CD PIE, RNA (5'-R(*GP*AP*GP*AP*CP*AP*UP*UP*GP*CP*AP*CSOLUTION NMR
    1EHT_A THEOPHYLLINE-BINDING RNASOLUTION NMR
    1EXY_A RNA APTAMER, 33-MERSOLUTION NMR
    1F1T_A MALACHITE GREEN APTAMER RNAX-RAY DIFFRACTION
    1FUF_AB (5'-R(*GP*GP*UP*AP*UP*UP*UP*CP*GP*GP*UP*AP*(CBR)P*X-RAY DIFFRACTION
    1HQ1_B 4.5S RNA DOMAIN IVX-RAY DIFFRACTION
    1J7T_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    1JU1_AB HIV-1Lai SL1SOLUTION NMR
    1LC4_AB 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UPX-RAY DIFFRACTION
    1M5L_A modified HIV-1 packaging signal stem-loop 1 RNASOLUTION NMR
    1MWL_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    1MZP_B fragment of 23S rRNAX-RAY DIFFRACTION
    1NBK_A RNA aptamerSOLUTION NMR
    1NLC_BA HIV-1 DIS(MAL) genomic RNAX-RAY DIFFRACTION
    1NTA_AB 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CPX-RAY DIFFRACTION
    1NTB_AB 5'-R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CPX-RAY DIFFRACTION
    1O15_A THEOPHYLLINE-BINDING RNASOLUTION NMR
    1O3Z_BA HIV-1 DIS(MAL) GENOMIC RNAX-RAY DIFFRACTION
    1O9M_AB EUBACTERIAL A-SITEX-RAY DIFFRACTION
    1P5M_A 55-MERSOLUTION NMR
    1Q8N_A RNA AptamerSOLUTION NMR
    1TXS_A Enteroviral 5'-UTRSOLUTION NMR
    1U3K_A ABISS7SOLUTION NMR
    1ULL_A RNA (5'-R (GP*GP*CP*UP*GP*GP*AP*CP*UP*CP*GP*UP*AP*SOLUTION NMR
    1WVD_BA 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CPX-RAY DIFFRACTION
    1Y6S_BA 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CPX-RAY DIFFRACTION
    1Y6T_BA 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CPX-RAY DIFFRACTION
    1Y73_BA 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CPX-RAY DIFFRACTION
    1Y90_BA 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CPX-RAY DIFFRACTION
    1Y95_BA 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CPX-RAY DIFFRACTION
    1Y99_AB 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CPX-RAY DIFFRACTION
    1YRJ_AB Bacterial 16 S Ribosomal RNA A Site OligonucleotidX-RAY DIFFRACTION
    2A9L_A ABISS7 RNASOLUTION NMR
    2BE0_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    2BEE_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    2D18_AB 5'-R(*GP*CP*UP*GP*AP*AP*GP*UP*GP*CP*AP*CP*AP*CP*GPSOLUTION NMR
    2ESI_AB 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UPX-RAY DIFFRACTION
    2ESJ_AB 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UPX-RAY DIFFRACTION
    2ET3_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    2ET4_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    2ET5_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    2ET8_AB 5'-R(*CP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GPX-RAY DIFFRACTION
    2F4S_AB 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AX-RAY DIFFRACTION
    2F4T_BA 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AX-RAY DIFFRACTION
    2F4U_AB 5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AX-RAY DIFFRACTION
    2FEY_A stem-loop IV of Tetrahymena telomerase RNASOLUTION NMR
    2FQN_AB 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*APX-RAY DIFFRACTION
    2G5K_AB 5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*APX-RAY DIFFRACTION
    2HUA_A CSFV IRES Domain IIaSOLUTION NMR
    2KTZ_A HCV IRES Domain IIa RNASOLUTION NMR
    2KU0_A HCV IRES Domain IIa RNASOLUTION NMR
    2KX8_A 7SKSOLUTION NMR
    2KZL_A RNA (55-MER)SOLUTION NMR
    2M57_A RNA_(35-MER)SOLUTION NMR
    2MQT_A RNA (68-MER)SOLUTION NMR
    2MQV_B RNA (68-MER)SOLUTION NMR
    2N6T_A RNA (42-MER)SOLUTION NMR
    2N6W_A RNA (68-MER)SOLUTION NMR
    2O3V_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*X-RAY DIFFRACTION
    2O3W_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*X-RAY DIFFRACTION
    2O3X_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*X-RAY DIFFRACTION
    2O3Y_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*X-RAY DIFFRACTION
    2OIJ_AB 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CPX-RAY DIFFRACTION
    2OIY_AB 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CPX-RAY DIFFRACTION
    2OJ0_AB 5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CPX-RAY DIFFRACTION
    2PN3_AB 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UPX-RAY DIFFRACTION
    2PWT_AB 22-mer of the ribosomal decoding siteX-RAY DIFFRACTION
    2PXB_B 4.5 S RNAX-RAY DIFFRACTION
    2PXD_B 4.5 S RNAX-RAY DIFFRACTION
    2PXE_B 4.5 S RNAX-RAY DIFFRACTION
    2PXF_B 4.5 S RNAX-RAY DIFFRACTION
    2PXK_B 4.5 S RNAX-RAY DIFFRACTION
    2PXL_B 4.5 S RNAX-RAY DIFFRACTION
    2PXP_B 4.5 S RNAX-RAY DIFFRACTION
    2PXQ_B 4.5 S RNAX-RAY DIFFRACTION
    2PXT_B 4.5 S RNAX-RAY DIFFRACTION
    2PXU_B 4.5 S RNAX-RAY DIFFRACTION
    2PXV_B 4.5 S RNAX-RAY DIFFRACTION
    2QEK_AB HIV-1 subtype F DIS genomic RNAX-RAY DIFFRACTION
    2XKV_B 4.5S RNAELECTRON MICROSCOPY
    357D_CBA RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*X-RAY DIFFRACTION
    364D_CBA RNA (5'-R(*CP*CP*CP*CP*AP*UP*GP*CP*GP*AP*GP*AP*GP*X-RAY DIFFRACTION
    3BNL_AB A site of bacterial ribosomeX-RAY DIFFRACTION
    3BNP_AB A site of bacterial ribosomeX-RAY DIFFRACTION
    3C44_AB HIV-1 subtype F genomic RNAX-RAY DIFFRACTION
    3DVV_AB HIV-1 genomic RNAX-RAY DIFFRACTION
    3FAR_AB RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*X-RAY DIFFRACTION
    3LOA_BA 5'-R(*CP*CP*GP*CP*GP*CP*CP*CP*GP*(5BU)P*CP*AP*CP*AX-RAY DIFFRACTION
    3LQX_B SRP RNAX-RAY DIFFRACTION
    3S4P_AB RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UPX-RAY DIFFRACTION
    3TD0_BA RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CPX-RAY DIFFRACTION
    3TD1_BA RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*(5BU)P*CPX-RAY DIFFRACTION
    3TZR_AB 5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CPX-RAY DIFFRACTION
    3WBM_XY RNA (25-MER)X-RAY DIFFRACTION
    3WRU_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*X-RAY DIFFRACTION
    3ZN8_G 4.5 S RNAELECTRON MICROSCOPY
    462D_BA RNA (5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*X-RAY DIFFRACTION
    4F8U_AB RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UPX-RAY DIFFRACTION
    4F8V_AB RNA (5'-R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UPX-RAY DIFFRACTION
    4GPW_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*X-RAY DIFFRACTION
    4GPX_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*X-RAY DIFFRACTION
    4GPY_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*X-RAY DIFFRACTION
    4K31_BC RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*X-RAY DIFFRACTION
    4K32_AB RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*X-RAY DIFFRACTION
    4P20_AB 5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UPX-RAY DIFFRACTION
    4P3S_BA 5'-D(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*AX-RAY DIFFRACTION
    4P3T_AB 5'-D(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)P*CP*GP*AX-RAY DIFFRACTION
    4PDB_I SELEX RNA aptamerX-RAY DIFFRACTION
    4PDQ_AB RNA (5'-*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GPX-RAY DIFFRACTION
    4PHY_AB RNA (26-MER)X-RAY DIFFRACTION
    4PMI_A Rev-Response-Element RNAX-RAY DIFFRACTION
    5EW4_BA RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*X-RAY DIFFRACTION
    5EW7_BA RNA (5'-R(*CP*CP*CP*CP*GP*GP*CP*CP*CP*CP*GP*GP*CP*X-RAY DIFFRACTION
    5M0H_A ASH1 E3 (42 NT-TL/TLR)X-RAY DIFFRACTION
    5OB3_A RNA aptamer (69-MER)X-RAY DIFFRACTION
    5VT0_R ESCHERICHIA COLI 6S RNA DERIVATIVE (112-MER)ELECTRON MICROSCOPY
    5ZEI_AB RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GX-RAY DIFFRACTION
    5ZEJ_AB RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GX-RAY DIFFRACTION
    5ZEM_AB RNA (5'-R(P*UP*GP*CP*GP*UP*CP*(1MA)P*CP*GP*UP*CP*GX-RAY DIFFRACTION
    6CF2_G RNA (35-MER)X-RAY DIFFRACTION
    1QZW_F 7S RNAX-RAY DIFFRACTION
    1R3E_DE 5'-R(*CP*UP*GP*UP*GP*UP*(FHU)P*CP*GP*AP*UP*CP*CP*AX-RAY DIFFRACTION
    1RY1_NM RNA (31-MER)ELECTRON MICROSCOPY
    2GJW_IJL 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GPX-RAY DIFFRACTION
    2NOK_CD 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UPX-RAY DIFFRACTION
    2NOQ_DC 18S ribosomal RNAELECTRON MICROSCOPY
    2NOQ_E 25S RIBOSOMAL RNAELECTRON MICROSCOPY
    2OM7_H Fragment of23S rRNA (H89)ELECTRON MICROSCOPY
    2OM7_I FRAGMENT OF23S RRNA (H42-44)ELECTRON MICROSCOPY
    2OM7_J Fragment of23S rRNA (H76)ELECTRON MICROSCOPY
    2PN4_AB 5'-R(*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UPX-RAY DIFFRACTION
    2WW9_D 25S RRNAELECTRON MICROSCOPY
    2WWA_D 25S RRNAELECTRON MICROSCOPY
    3BNN_CD A site of human ribosomeX-RAY DIFFRACTION
    3BNO_AB A site of human mitochondrial ribosomeX-RAY DIFFRACTION
    3BNQ_AB A site of human mitochondrial ribosomeX-RAY DIFFRACTION
    3BNR_AB A site of human mitochondrial ribosomeX-RAY DIFFRACTION
    3BNS_AB A site of human mitochondrial ribosomeX-RAY DIFFRACTION
    3J0D_hH ribosomal 16S RNAELECTRON MICROSCOPY
    3J0E_eE ribosomal 16S RNAELECTRON MICROSCOPY
    3J0L_7 60S RIBOSOMAL RNA FRAGMENTELECTRON MICROSCOPY
    3J0L_1 60S RIBOSOMAL RNA FRAGMENTELECTRON MICROSCOPY
    3J0O_7 60S ribosomal RNA fragmentELECTRON MICROSCOPY
    3J0P_7 60S RIBOSOMAL RNA FRAGMENTELECTRON MICROSCOPY
    3J0Q_7 60S RIBOSOMAL RNA FRAGMENTELECTRON MICROSCOPY
    3J46_4 23S ribosomal RNAELECTRON MICROSCOPY
    3JCM_E SNR14 SNRNAELECTRON MICROSCOPY
    4CXG_2 28S RRNA - H89ELECTRON MICROSCOPY
    4CXH_2 28S RRNA - H89ELECTRON MICROSCOPY
    4JRC_B Distal Stem I region of the glyQS T box leader RNAX-RAY DIFFRACTION
    4WCE_Y 5S RRNAX-RAY DIFFRACTION
    4WFA_Y 5S RRNAX-RAY DIFFRACTION
    4WFB_Y 5S RRNAX-RAY DIFFRACTION
    4ZC7_AB RNA duplexX-RAY DIFFRACTION
    5BTM_A RNA (55-mer)X-RAY DIFFRACTION
    5BWS_AB RNA (5'-D(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*X-RAY DIFFRACTION
    5BXK_CD RNA (5'-D(P*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GPX-RAY DIFFRACTION
    5FJ0_AB HMKT-7X-RAY DIFFRACTION
    5G4U_IJ HMKT-7X-RAY DIFFRACTION
    5G4V_AB HMKT-7X-RAY DIFFRACTION
    5GAD_1 ESRP 4.5S RNAELECTRON MICROSCOPY
    5GAF_1 SRP 4.5S RNAELECTRON MICROSCOPY
    5GAG_1 SRP 4.5S RNAELECTRON MICROSCOPY
    5GAH_1 SRP 4.5S RNAELECTRON MICROSCOPY
    5HKV_Y 5S RIBOSOMAL RNAX-RAY DIFFRACTION
    5HL7_Y 5S RIBOSOMAL RNAX-RAY DIFFRACTION
    5NRG_Y 5S RIBOSOMAL RNAX-RAY DIFFRACTION
    5T7V_C 5S ribosomal RNAELECTRON MICROSCOPY
    5TF6_B U6 snRNAX-RAY DIFFRACTION
    5V1L_CD RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*(ZTH)P*AP*GP*CP*G)X-RAY DIFFRACTION
    5XZ1_AB RNA (5'-R(*UP*GP*CP*GP*UP*CP*GP*CP*UP*CP*CP*GP*GP*X-RAY DIFFRACTION
    5Y7M_D RNA (52-MER)X-RAY DIFFRACTION
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