RNA 3D Hub //

Equivalence class NR_20.0_52978.2 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
16N6C|1|D (rep)RNA (5'-R(P*AP*A)-3')synthetic constructVibrio cholerae Oligoribonuclease bound to pAAX-ray diffraction1.6222019-06-12
26N6J|1|CRNA (5'-R(P*AP*A)-3')synthetic constructHuman REXO2 bound to pAAX-ray diffraction1.3222019-06-12
36N6J|1|DRNA (5'-R(P*AP*A)-3')synthetic constructHuman REXO2 bound to pAAX-ray diffraction1.3222019-06-12
47MPM|1|B5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
57MPM|1|H5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
67MPM|1|L5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
77MPM|1|F5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
87MPM|1|J5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
97MPM|1|D5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
107MPM|1|P5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
117MPM|1|N5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
126P7Q|1|ERNA (5'-R(P*AP*A)-3')Escherichia coliStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-ray diffraction1.6622019-12-25
136P7Q|1|FRNA (5'-R(P*AP*A)-3')Escherichia coliStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-ray diffraction1.6622019-12-25
146P7Q|1|DRNA (5'-R(P*AP*A)-3')Escherichia coliStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-ray diffraction1.6622019-12-25
158JBB|1|DRNA (5'-R(*AP*(A23))-3')synthetic constructCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-ray diffraction1.8122023-12-13
165XSP|1|CDNA (5'-R(P*AP*A)-3')synthetic constructThe catalytic domain of GdpP with 5'-pApAX-ray diffraction2.14622018-01-31
175XSP|1|DDNA (5'-R(P*AP*A)-3')synthetic constructThe catalytic domain of GdpP with 5'-pApAX-ray diffraction2.14622018-01-31
186RCL|1|CRNA (5'-R(P*AP*A)-3')synthetic constructCrystal structure of REXO2-D199A-AAX-ray diffraction1.9722019-10-09
198JBB|1|CRNA (5'-R(*AP*(A23))-3')synthetic constructCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-ray diffraction1.8122023-12-13
205JJU|1|CRNA (5'-R(P*AP*A)-3')synthetic constructCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-ray diffraction2.3122016-05-04
218Y7G|1|ERNA (5'-R(P*AP*A)-3')Marinitoga sp. 1155Crystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)X-ray diffraction3.1522024-07-17
228Y7G|1|DRNA (5'-R(P*AP*A)-3')Marinitoga sp. 1155Crystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)X-ray diffraction3.1522024-07-17
239MMW|1|QRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
249MMW|1|DRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
259MMW|1|CRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
269MMW|1|TRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
279MMW|1|IRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
289MMW|1|JRNA (5'-R(*AP*(A23))-3')Thermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapElectron microscopy2.3622025-11-12
299OFE|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
309OFD|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
319OFC|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
329OFC|1|NcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
339OFC|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
349OFE|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
359OFB|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapElectron microscopy2.6822025-08-20
369OFD|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
379OFC|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
389OFC|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
399OFB|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapElectron microscopy2.6822025-08-20
409OFE|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
413J0L|1|wmRNA fragmentOryctolagus cuniculusCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9.8A cryo-EM map: classic PRE state 1Electron microscopy9.822011-11-16
423J0O|1|wmRNA fragmentOryctolagus cuniculusCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9A cryo-EM map: classic PRE state 2Electron microscopy922011-11-16
439OFE|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
449OFC|1|McA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
453J0Q|1|wmRNA fragmentOryctolagus cuniculusCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 2Electron microscopy10.622011-11-16
464EJT|1|G5'-R(*AP*A)-3'Staphylococcus epidermidis TcaR in complex with RNAX-ray diffraction322013-06-05
473J0P|1|wmRNA fragmentOryctolagus cuniculusCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 1Electron microscopy10.622011-11-16

Release history

Release4.13
Date2025-11-12

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.

#SViewPDBTitleMethodResolution#NTs
16N6C|1|DVibrio cholerae Oligoribonuclease bound to pAAX-RAY DIFFRACTION1.622
29MMW|1|CCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
39OFD|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
45XSP|1|DThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
57MPM|1|DBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
67MPM|1|FBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
79OFC|1|NCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
89OFB|1|CCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
95XSP|1|CThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
106RCL|1|CCrystal structure of REXO2-D199A-AAX-RAY DIFFRACTION1.972
118JBB|1|DCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
129OFE|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
138JBB|1|CCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
149OFC|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
157MPM|1|NBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
163J0P|1|wCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 1ELECTRON MICROSCOPY10.62
173J0O|1|wCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9A cryo-EM map: classic PRE state 2ELECTRON MICROSCOPY92
183J0Q|1|wCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 10.6A cryo-em map: rotated PRE state 2ELECTRON MICROSCOPY10.62
193J0L|1|wCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9.8A cryo-EM map: classic PRE state 1ELECTRON MICROSCOPY9.82
204EJT|1|GStaphylococcus epidermidis TcaR in complex with RNAX-RAY DIFFRACTION32
219OFE|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
226N6J|1|CHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
239OFE|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
249OFB|1|DCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
258Y7G|1|DCrystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)X-RAY DIFFRACTION3.152
265JJU|1|CCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-RAY DIFFRACTION2.312
279MMW|1|DCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
289OFC|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
296P7Q|1|EStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
309MMW|1|JCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
317MPM|1|HBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
329MMW|1|ICRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
337MPM|1|LBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
348Y7G|1|ECrystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)X-RAY DIFFRACTION3.152
359MMW|1|QCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
369OFC|1|MCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
376P7Q|1|FStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
389OFC|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
399OFE|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
409OFD|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
417MPM|1|PBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
429MMW|1|TCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
439OFC|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
446P7Q|1|DStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
456N6J|1|DHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
467MPM|1|BBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
477MPM|1|JBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.


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