RNA 3D Hub //

Equivalence class NR_3.0_64918.26 Obsolete

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
17SOS|1|B (rep)RNA (5'-R(*AP*AP*AP*A)-3')synthetic constructLaM domain of human LARP1 in complex with AAAA RNAX-ray diffraction1.2542022-08-03
26SCE|1|Bcyclic oligoadenylatesynthetic constructStructure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylateX-ray diffraction1.8342020-02-19
36XL1|1|CcA4synthetic constructcrystal structure of cA4-activated Cad1(D294N)X-ray diffraction1.9542020-12-30
48Q42|1|XCyclic tetraadenosine monophosphate (cA4)synthetic constructCrystal structure of cA4-bound Can2 (E341A) in complex with oligo-A DNAX-ray diffraction1.9742023-11-22
56SCF|1|Icyclic oligoadenylatesynthetic constructA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-ray diffraction1.5542019-10-30
66SCF|1|Kcyclic oligoadenylatesynthetic constructA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-ray diffraction1.5542019-10-30
76YUD|1|Kcyclic tetra-adenylate (cA4)synthetic constructStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-ray diffraction1.8442020-08-19
86YUD|1|Ocyclic tetra-adenylate (cA4)synthetic constructStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-ray diffraction1.8442020-08-19
96SCF|1|Mcyclic oligoadenylatesynthetic constructA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-ray diffraction1.5542019-10-30
106YUD|1|Pcyclic tetra-adenylate (cA4)synthetic constructStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-ray diffraction1.8442020-08-19
116SCF|1|Lcyclic oligoadenylatesynthetic constructA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-ray diffraction1.5542019-10-30
126YUD|1|Mcyclic tetra-adenylate (cA4)synthetic constructStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-ray diffraction1.8442020-08-19
136YUD|1|Qcyclic tetra-adenylate (cA4)synthetic constructStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-ray diffraction1.8442020-08-19
148Q44|1|XCyclic tetraadenosine monophosphate (cA4)synthetic constructCrystal structure of cA4-bound Can2 (E364R) in complex with oligo-T DNAX-ray diffraction2.342023-11-22
158Q40|1|XCyclic tetraadenosine monophosphate (cA4)synthetic constructCrystal structure of cA4 activated Can2 in complex with a cleaved DNA substrateX-ray diffraction2.2142023-11-22
168Q41|1|XCyclic tetraadenosine monophosphate (cA4)synthetic constructCrystal structure of Can2 (E341A) bound to cA4 and TTTAAA ssDNAX-ray diffraction2.3842023-11-22
176WXQ|1|Ecyclic tetraadenylatesynthetic constructCrystal structure of CRISPR-associated transcription factor Csa3 complexed with cA4X-ray diffraction2.0542021-11-17
188Q43|1|XCyclic tetraadenosine monophosphate (cA4)synthetic constructCrystal structure of cA4-bound Can2 (E341A) in complex with oligo-C DNAX-ray diffraction2.2842023-11-22
198QJK|1|CCyclic tetraadenosine monophosphate (cA4)synthetic constructStructure of the cytoplasmic domain of csx23 from Vibrio cholera in complex with cyclic tetra-adenylate (cA4)X-ray diffraction1.76142024-08-07
208BAO|1|CCyclic tetra-adenylate (cA4)synthetic constructDysgonamonadaceae bacterium CRISPR ancillary nuclease 2X-ray diffraction2.0642022-11-30
216O6X|1|DCyclic RNA cA4synthetic constructCrystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallizationX-ray diffraction2.1142019-07-31
227BDV|1|Fcyclic tetra-adenylatesynthetic constructStructure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4)X-ray diffraction2.0242021-03-03
238B0R|1|DRNA (5'-R(P*AP*AP*AP*A)-3')SulfurihydrogenibiumStructure of the CalpL/cA4 complexX-ray diffraction2.242022-11-16
247BDV|1|Hcyclic tetra-adenylatesynthetic constructStructure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4)X-ray diffraction2.0242021-03-03
256O6X|1|CCyclic RNA cA4synthetic constructCrystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallizationX-ray diffraction2.1142019-07-31
266O7B|1|CCyclic RNA cA4synthetic constructCrystal structure of Csm1-Csm4 cassette in complex with cA4X-ray diffraction2.442019-07-31
276O6V|1|CCyclic RNA cA4synthetic constructCrystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6X-ray diffraction2.3542019-07-31
286WXX|1|YcA4synthetic constructcrystal structure of cA4-activated Cad1X-ray diffraction342020-12-30
296WXX|1|XcA4synthetic constructcrystal structure of cA4-activated Cad1X-ray diffraction342020-12-30
306R9R|1|DDNA (5'-R(P*AP*AP*AP*A)-3')synthetic constructCrystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2X-ray diffraction2.742019-10-02
318JH1|1|CRNA (5'-R(P*AP*AP*AP*A)-3')synthetic constructCrystal Structure of the Csm6 Y161A mutant from Thermus thermophilus HB8 in complex with cyclic-tetraadenylate (cA4)X-ray diffraction2.8942023-12-13
326OV0|1|ERNA (5'-R(*AP*AP*AP*(A23))-3')synthetic constructCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-ray diffraction2.842019-07-31
337YGL|1|CRNA (5'-R(*AP*AP*AP*(A23))-3')synthetic constructCrystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with A4>p cleavage intermediateX-ray diffraction2.542023-02-15
346OV0|1|HRNA (5'-R(*AP*AP*AP*(A23))-3')synthetic constructCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-ray diffraction2.842019-07-31
359GU5|1|MRNA (5'-R(P*AP*AP*AP*A)-3')RNA interference vector pBSK-GusCrystal Structure of Hfq V22AX-ray diffraction2.942025-02-05
366OV0|1|GRNA (5'-R(*AP*AP*AP*(A23))-3')synthetic constructCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-ray diffraction2.832019-07-31
376O6V|1|DCyclic RNA cA4synthetic constructCrystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6X-ray diffraction2.3542019-07-31
386OV0|1|FRNA (5'-R(*AP*AP*AP*(A23))-3')synthetic constructCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-ray diffraction2.832019-07-31
396O7B|1|DCyclic RNA cA4synthetic constructCrystal structure of Csm1-Csm4 cassette in complex with cA4X-ray diffraction2.442019-07-31
406R9R|1|EDNA (5'-R(P*AP*AP*AP*A)-3')synthetic constructCrystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2X-ray diffraction2.722019-10-02
417Z55|1|CCCCyclic RNA cA4synthetic constructCrystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in complex with its substrateX-ray diffraction1.66442022-11-23
429EYJ|1|DcA4synthetic constructCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to cA4Electron microscopy2.9742024-10-02
439EYI|1|EA4p (5'-R(*AP*AP*AP*AP)-3')synthetic constructCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4pElectron microscopy2.7542024-10-02
449EYK|1|DA4>p (5'-R(*AP*AP*AP*(A23))-3')synthetic constructCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4>pElectron microscopy2.8442024-10-02
459EYK|1|EA4>p (5'-R(*AP*AP*AP*(A23))-3')synthetic constructCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4>pElectron microscopy2.8442024-10-02
469EYI|1|DA4p (5'-R(*AP*AP*AP*AP)-3')synthetic constructCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4pElectron microscopy2.7542024-10-02
476O7H|1|KCyclic DNA cA4synthetic constructCryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas systemElectron microscopy2.942019-07-31

Release history

Release3.3733.3743.3753.3763.377
Date2025-02-052025-02-122025-02-192025-02-262025-03-05

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
19GU5|1|MCrystal Structure of Hfq V22AX-RAY DIFFRACTION2.94
26O7B|1|CCrystal structure of Csm1-Csm4 cassette in complex with cA4X-RAY DIFFRACTION2.44
36OV0|1|ECrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-RAY DIFFRACTION2.84
46OV0|1|HCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-RAY DIFFRACTION2.84
59EYK|1|DCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4>pELECTRON MICROSCOPY2.844
69EYK|1|ECryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4>pELECTRON MICROSCOPY2.844
79EYJ|1|DCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to cA4ELECTRON MICROSCOPY2.974
89EYI|1|ECryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4pELECTRON MICROSCOPY2.754
99EYI|1|DCryo-EM structure of SAVED-Lon protease CCaCalpL filament bound to A4pELECTRON MICROSCOPY2.754
108B0R|1|DStructure of the CalpL/cA4 complexX-RAY DIFFRACTION2.24
118BAO|1|CDysgonamonadaceae bacterium CRISPR ancillary nuclease 2X-RAY DIFFRACTION2.064
127BDV|1|FStructure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION2.024
138Q40|1|XCrystal structure of cA4 activated Can2 in complex with a cleaved DNA substrateX-RAY DIFFRACTION2.214
148Q41|1|XCrystal structure of Can2 (E341A) bound to cA4 and TTTAAA ssDNAX-RAY DIFFRACTION2.384
158Q44|1|XCrystal structure of cA4-bound Can2 (E364R) in complex with oligo-T DNAX-RAY DIFFRACTION2.34
168Q42|1|XCrystal structure of cA4-bound Can2 (E341A) in complex with oligo-A DNAX-RAY DIFFRACTION1.974
178Q43|1|XCrystal structure of cA4-bound Can2 (E341A) in complex with oligo-C DNAX-RAY DIFFRACTION2.284
187YGL|1|CCrystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with A4>p cleavage intermediateX-RAY DIFFRACTION2.54
198JH1|1|CCrystal Structure of the Csm6 Y161A mutant from Thermus thermophilus HB8 in complex with cyclic-tetraadenylate (cA4)X-RAY DIFFRACTION2.894
206WXQ|1|ECrystal structure of CRISPR-associated transcription factor Csa3 complexed with cA4X-RAY DIFFRACTION2.054
216SCF|1|IA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-RAY DIFFRACTION1.554
226R9R|1|DCrystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2X-RAY DIFFRACTION2.74
236SCE|1|BStructure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylateX-RAY DIFFRACTION1.834
246YUD|1|MStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION1.844
256YUD|1|QStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION1.844
266YUD|1|OStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION1.844
276YUD|1|PStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION1.844
286YUD|1|KStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION1.844
296O6V|1|CCrystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6X-RAY DIFFRACTION2.354
306O6X|1|DCrystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallizationX-RAY DIFFRACTION2.114
317Z55|1|CCCCrystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in complex with its substrateX-RAY DIFFRACTION1.6644
326XL1|1|Ccrystal structure of cA4-activated Cad1(D294N)X-RAY DIFFRACTION1.954
336WXX|1|Ycrystal structure of cA4-activated Cad1X-RAY DIFFRACTION34
346WXX|1|Xcrystal structure of cA4-activated Cad1X-RAY DIFFRACTION34
357BDV|1|HStructure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION2.024
368QJK|1|CStructure of the cytoplasmic domain of csx23 from Vibrio cholera in complex with cyclic tetra-adenylate (cA4)X-RAY DIFFRACTION1.7614
376O7B|1|DCrystal structure of Csm1-Csm4 cassette in complex with cA4X-RAY DIFFRACTION2.44
386O7H|1|KCryo-EM structure of Csm-crRNA-target RNA ternary complex in complex with cA4 in type III-A CRISPR-Cas systemELECTRON MICROSCOPY2.94
396SCF|1|MA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-RAY DIFFRACTION1.554
406SCF|1|KA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-RAY DIFFRACTION1.554
416SCF|1|LA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylateX-RAY DIFFRACTION1.554
426O6V|1|DCrystal structure of Csm6 in complex with cA4 by soaking cA4 into Csm6X-RAY DIFFRACTION2.354
437SOS|1|BLaM domain of human LARP1 in complex with AAAA RNAX-RAY DIFFRACTION1.254
446O6X|1|CCrystal structure of Csm6 W14A/E337A mutant in complex with cA4 by cocrystallizationX-RAY DIFFRACTION2.114
456OV0|1|GCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-RAY DIFFRACTION2.83
466R9R|1|ECrystal structure of Csx1 in complex with cyclic oligoadenylate cOA4 conformation 2X-RAY DIFFRACTION2.72
476OV0|1|FCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6X-RAY DIFFRACTION2.83

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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