RNA 3D Hub //

Equivalence class NR_4.0_52978.3 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
215JJU|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
228Y7G|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
238Y7G|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
249MMW|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
259MMW|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
269MMW|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
279MMW|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
289MMW|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
299MMW|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
309OFE|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
319OFD|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
329OFC|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
339OFC|1|NcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
349OFC|1|JcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
359OFE|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
369OFB|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
379OFD|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerElectron microscopy2.8622025-08-20
389OFC|1|DcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
399OFC|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
409OFB|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
419OFE|1|CcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
429OFE|1|IcA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersElectron microscopy2.6822025-08-20
439OFC|1|McA4 cleavage product, A2>PThermoanaerobaculum aquaticumCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersElectron microscopy3.1722025-08-20
444EJT|1|G5'-R(*AP*A)-3'Staphylococcus epidermidis TcaR in complex with RNAX-ray diffraction322013-06-05

Release history

Release4.18
Date2025-12-17

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
16RCL|1|CCrystal structure of REXO2-D199A-AAX-RAY DIFFRACTION1.972
27MPM|1|BBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
39OFD|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
49OFB|1|DCryoEM structure of Cad1 bound with cA4 and ATP, symmetry expanded dimer refined against a composite mapELECTRON MICROSCOPY2.682
59OFE|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
69OFC|1|JCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
79OFC|1|NCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
88JBB|1|CCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
99MMW|1|CCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
109MMW|1|QCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
117MPM|1|HBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
126N6J|1|DHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
139MMW|1|DCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
149OFC|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
157MPM|1|DBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
165O4Z|1|BStructure of the inactive T.maritima PDE (TM1595) D80N D154N mutant with substrate 5'-pApAX-RAY DIFFRACTION1.72
179OFE|1|ICryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
186P7Q|1|DStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
197MPM|1|FBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
207MPM|1|JBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
219OFD|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with one intact dimerELECTRON MICROSCOPY2.862
228Y7G|1|ECrystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)X-RAY DIFFRACTION3.152
239OFC|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
249OFB|1|CCryoEM 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
269MMW|1|ICRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
279MMW|1|TCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
286P7Q|1|FStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
296P7Q|1|EStructure of E. coli MS115-1 NucC, 5'-pApA bound formX-RAY DIFFRACTION1.662
307MPM|1|LBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
314EJT|1|GStaphylococcus epidermidis TcaR in complex with RNAX-RAY DIFFRACTION32
325JJU|1|CCrystal structure of Rv2837c complexed with 5'-pApA and 5'-AMPX-RAY DIFFRACTION2.312
337MPM|1|NBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
349OFE|1|DCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
359OFE|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimersELECTRON MICROSCOPY2.682
365XSP|1|CThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
375XSP|1|DThe catalytic domain of GdpP with 5'-pApAX-RAY DIFFRACTION2.1462
387MPM|1|PBartonella henselae NrnC bound to pAAX-RAY DIFFRACTION1.952
399OFC|1|MCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172
406N6C|1|DVibrio cholerae Oligoribonuclease bound to pAAX-RAY DIFFRACTION1.622
416N6J|1|CHuman REXO2 bound to pAAX-RAY DIFFRACTION1.322
429MMW|1|JCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus mapELECTRON MICROSCOPY2.362
438JBB|1|DCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>pX-RAY DIFFRACTION1.812
449OFC|1|CCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with three intact dimersELECTRON MICROSCOPY3.172

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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