RNA 3D Hub //

Equivalence class NR_all_52978.4 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
115O4Z|1|BRNA 5'-pApAsynthetic constructStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApAX-ray diffraction1.722017-10-25
127MPM|1|N5'-phosphorylated AAsynthetic constructBartonella henselae NrnC bound to pAAX-ray diffraction1.9522021-09-15
136P7Q|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
146P7Q|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
156P7Q|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
168JBB|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
175XSP|1|CDNA (5'-R(P*AP*A)-3')synthetic constructThe catalytic domain of GdpP with 5'-pApAX-ray diffraction2.14622018-01-31
185XSP|1|DDNA (5'-R(P*AP*A)-3')synthetic constructThe catalytic domain of GdpP with 5'-pApAX-ray diffraction2.14622018-01-31
196RCL|1|CRNA (5'-R(P*AP*A)-3')synthetic constructCrystal structure of REXO2-D199A-AAX-ray diffraction1.9722019-10-09
208JBB|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
219EBT|1|CTetra-adenylateThermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapElectron microscopy2.3622026-01-07
229EBT|1|DTetra-adenylateThermoanaerobaculum aquaticumCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapElectron microscopy2.3622026-01-07
235JJU|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
248Y7G|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
258Y7G|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
269MMW|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
279MMW|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
289MMW|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
299MMW|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
309MMW|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
319MMW|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
329OFE|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
339OFD|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
349OFC|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
359OFC|1|NcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
369OFC|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
379OFE|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
389OFB|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
399OFD|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
409OFC|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
419OFC|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
429OFB|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
439OFE|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
443J0L|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
453J0O|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
469OFE|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
479OFC|1|McA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
483J0Q|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
494EJT|1|G5'-R(*AP*A)-3'Staphylococcus epidermidis TcaR in complex with RNAX-ray diffraction322013-06-05
503J0P|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

Release4.21
Date2026-01-07

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
18Y7G|1|ECrystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)X-RAY DIFFRACTION3.152
25JJU|1|CCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-RAY DIFFRACTION2.312
39MMW|1|QCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
49EBT|1|DCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapELECTRON MICROSCOPY2.362
59MMW|1|DCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
68Y7G|1|DCrystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)X-RAY DIFFRACTION3.152
79MMW|1|CCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
89OFE|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
97MPM|1|FBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
107MPM|1|PBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
119OFE|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
126N6J|1|CHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
139OFC|1|MCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
147MPM|1|JBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
157MPM|1|NBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
167MPM|1|HBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
177MPM|1|DBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
185O4Z|1|BStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApAX-RAY DIFFRACTION1.72
196P7Q|1|FStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
206P7Q|1|EStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
216N6J|1|DHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
224EJT|1|GStaphylococcus epidermidis TcaR in complex with RNAX-RAY DIFFRACTION32
233J0O|1|wCore of mammalian 80S pre-ribosome in complex with tRNAs fitted to a 9A cryo-EM map: classic PRE state 2ELECTRON MICROSCOPY92
243J0P|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
253J0Q|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
263J0L|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
276N6C|1|DVibrio cholerae Oligoribonuclease bound to pAAX-RAY DIFFRACTION1.622
287MPM|1|LBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
297MPM|1|BBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
309OFD|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
319OFC|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
329OFB|1|CCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
339OFB|1|DCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
349OFE|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
359OFC|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
369OFC|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
375XSP|1|DThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
388JBB|1|DCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
396RCL|1|CCrystal structure of REXO2-D199A-AAX-RAY DIFFRACTION1.972
408JBB|1|CCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
419EBT|1|CCRISPR-associated deaminase Cad1 in cA4 bound form, symmetry expanded dimer, refined against a composite mapELECTRON MICROSCOPY2.362
426P7Q|1|DStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
435XSP|1|CThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
449OFD|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
459MMW|1|TCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
469OFC|1|NCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
479MMW|1|JCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
489MMW|1|ICRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
499OFC|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
509OFE|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682

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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