RNA 3D Hub //

Equivalence class NR_3.5_74924.30 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
13PEY|1|B (rep)RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')S. cerevisiae Dbp5 bound to RNA and ADP BeF3X-ray diffraction1.462011-03-23
23PEW|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')S. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3X-ray diffraction1.562011-03-23
35ELX|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Saccharomyces cerevisiaeS. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3X-ray diffraction1.8162016-02-24
44ALP|1|EHEXA URIDINEsynthetic constructThe Lin28b Cold shock domain in complex with hexauridineX-ray diffraction1.4862012-09-05
55SZE|1|CRNA (5'-R(P*UP*UP*U)-3')unidentifiedCrystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5AX-ray diffraction1.532017-04-12
62HYI|1|F5'-R(*UP*UP*UP*UP*UP*U)-3'Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-ray diffraction2.362006-08-15
73O8C|1|CRNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3')Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-ray diffraction262011-01-05
86G2K|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructStructure of HuR RRM3 in complex with RNA (UUUUUU)X-ray diffraction2.0162018-10-31
92HYI|1|L5'-R(*UP*UP*UP*UP*UP*U)-3'Structure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-ray diffraction2.362006-08-15
106M7D|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructStructure of ncleoprotein of sendai virusElectron microscopy2.962021-03-24
116WRE|1|DRNA (5'-R(*UP*(U37)P*(U37)P*UP)-3')Homo sapiensCrystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ionX-ray diffraction252020-05-13
125BTE|1|DRNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')Homo sapiensCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-ray diffraction2.462015-07-22
135BTE|1|CRNA (5'-R(P*UP*(U37)P*(U37)P*UP*UP*U)-3')Homo sapiensCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-ray diffraction2.462015-07-22
143EX7|1|JRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')The crystal structure of EJC in its transition stateX-ray diffraction2.362008-12-09
153EX7|1|FRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')The crystal structure of EJC in its transition stateX-ray diffraction2.362008-12-09
163PF5|1|Rhexaribouracil (rU6)Crystal structure of Bs-CspB in complex with rU6X-ray diffraction1.6852011-09-21
176I0U|1|BRNA (5'-R(*UP*UP*UP*U)-3')Drosophila melanogasterCrystal structure of DmTailor in complex with U6 RNAX-ray diffraction242018-12-05
188RDV|1|YHeterogenous mRNAPsychrobacter urativoransCryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon, mRNA and P-site tRNA (structure 2).Electron microscopy2.662024-02-21
193O8R|1|CRNA (5'-R(P*UP*(5BU)P*UP*UP*UP*U)-3')Visualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-ray diffraction2.362011-01-05
207EXA|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Escherichia coliStructure of mumps virus nucleoprotein without C-armElectron microscopy2.962024-08-21
217SOW|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructLaM domain of human LARP1 in complex with UUUUUUX-ray diffraction1.342022-11-09
225ZSA|1|CRNA (5'-R(P*UP*UP*UP*U)-3')synthetic constructCrystal structure of monkey TLR7 in complex with IMDQ and UUUUUUX-ray diffraction2.542019-01-30
235ZSA|1|DRNA (5'-R(P*UP*UP*UP*U)-3')synthetic constructCrystal structure of monkey TLR7 in complex with IMDQ and UUUUUUX-ray diffraction2.542019-01-30
247F1M|1|SRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructMarburg virus nucleoprotein-RNA complexElectron microscopy3.162022-03-09
257F1M|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructMarburg virus nucleoprotein-RNA complexElectron microscopy3.162022-03-09
268CBW|1|1RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Escherichia coli BL21(DE3)CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid assembly monomerElectron microscopy3.48562024-06-26
277YPW|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructLloviu cuevavirus nucleoprotein-RNA complexElectron microscopy3.035662023-04-19
287EWQ|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Mumps orthorubulavirusStructure of Mumps virus nucleocapsid ringElectron microscopy3.562021-06-23
297ZNJ|1|jRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
307ZNJ|1|ORNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
316CAP|1|YRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')Thermus thermophilusCrystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with SisomicinX-ray diffraction3.462018-07-25
327ZNJ|1|JRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
337ZNJ|1|oRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
347ZNJ|1|eRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
357ZNJ|1|ERNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
369FIA|1|bVulr20Toxoplasma gondiiSSU(body) structure derived from the SSU sample of the mitoribosome from T. gondii.Electron microscopy3.2962024-12-11
374NL3|1|Z5'-R(*UP*UP*UP*UP*UP*U)-3'Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-ray diffraction3.162014-09-10
384Y91|1|ORNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructCrystal Structure of a Thermotoga maritima Hfq homologX-ray diffraction2.6662016-03-16
398VFT|1|wmRNAOryctolagus cuniculusTranslating 80S rabbit ribosome stalled by emetine with eEF2Electron microscopy3.362024-12-25
404Y91|1|NRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructCrystal Structure of a Thermotoga maritima Hfq homologX-ray diffraction2.6662016-03-16
416CAS|1|YRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')Thermus thermophilusSerial Femtosecond X-ray Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with N1MSX-ray diffraction3.562018-07-25
426CAR|1|YRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')Thermus thermophilusSerial Femtosecond X-ray Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with SisomicinX-ray diffraction3.462018-07-25
431N33|1|ZA-SITE MESSENGER RNA FRAGMENTThermus thermophilusStructure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycinX-ray diffraction3.3542002-11-29
444NL3|1|R5'-R(*UP*UP*UP*UP*UP*U)-3'Crystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-ray diffraction3.162014-09-10
453PF5|1|Shexaribouracil (rU6)Crystal structure of Bs-CspB in complex with rU6X-ray diffraction1.6812011-09-21
467YR8|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructLloviu cuevavirus nucleoprotein(1-450 residues)-RNA complexElectron microscopy3.262023-04-19
476PPN|1|AMimic of unprocessed U6 snRNAsynthetic constructStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-ray diffraction1.9152020-06-17
486PPN|1|IMimic of unprocessed U6 snRNAsynthetic constructStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-ray diffraction1.9152020-06-17

Release history

Release4.45
Date2026-06-24

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
13PF5|1|SCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.681
23O8C|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION26
33PF5|1|RCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.685
48RDV|1|YCryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon, mRNA and P-site tRNA (structure 2).ELECTRON MICROSCOPY2.66
58VFT|1|wTranslating 80S rabbit ribosome stalled by emetine with eEF2ELECTRON MICROSCOPY3.36
67YPW|1|RLloviu cuevavirus nucleoprotein-RNA complexELECTRON MICROSCOPY3.03566
77YR8|1|RLloviu cuevavirus nucleoprotein(1-450 residues)-RNA complexELECTRON MICROSCOPY3.26
87F1M|1|RMarburg virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.16
97F1M|1|SMarburg virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.16
108CBW|1|1CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid assembly monomerELECTRON MICROSCOPY3.4856
117EWQ|1|BStructure of Mumps virus nucleocapsid ringELECTRON MICROSCOPY3.56
126M7D|1|BStructure of ncleoprotein of sendai virusELECTRON MICROSCOPY2.96
137EXA|1|BStructure of mumps virus nucleoprotein without C-armELECTRON MICROSCOPY2.96
142HYI|1|LStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
152HYI|1|FStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
163EX7|1|JThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
177ZNJ|1|OStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
187ZNJ|1|jStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
197ZNJ|1|eStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
207ZNJ|1|JStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
217ZNJ|1|EStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
227ZNJ|1|oStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
233EX7|1|FThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
243PEY|1|BS. cerevisiae Dbp5 bound to RNA and ADP BeF3X-RAY DIFFRACTION1.46
255ELX|1|BS. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3X-RAY DIFFRACTION1.816
263PEW|1|BS. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3X-RAY DIFFRACTION1.56
276CAP|1|YCrystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with SisomicinX-RAY DIFFRACTION3.46
286CAS|1|YSerial Femtosecond X-ray Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with N1MSX-RAY DIFFRACTION3.56
296CAR|1|YSerial Femtosecond X-ray Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with SisomicinX-RAY DIFFRACTION3.46
301N33|1|ZStructure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycinX-RAY DIFFRACTION3.354
315BTE|1|CCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.46
325BTE|1|DCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.46
336I0U|1|BCrystal structure of DmTailor in complex with U6 RNAX-RAY DIFFRACTION24
349FIA|1|bVSSU(body) structure derived from the SSU sample of the mitoribosome from T. gondii.ELECTRON MICROSCOPY3.296
353O8R|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION2.36
366WRE|1|DCrystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ionX-RAY DIFFRACTION25
376G2K|1|RStructure of HuR RRM3 in complex with RNA (UUUUUU)X-RAY DIFFRACTION2.016
386PPN|1|IStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-RAY DIFFRACTION1.915
396PPN|1|AStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-RAY DIFFRACTION1.915
404Y91|1|NCrystal Structure of a Thermotoga maritima Hfq homologX-RAY DIFFRACTION2.666
414Y91|1|OCrystal Structure of a Thermotoga maritima Hfq homologX-RAY DIFFRACTION2.666
424NL3|1|RCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-RAY DIFFRACTION3.16
434NL3|1|ZCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-RAY DIFFRACTION3.16
445ZSA|1|DCrystal structure of monkey TLR7 in complex with IMDQ and UUUUUUX-RAY DIFFRACTION2.54
455ZSA|1|CCrystal structure of monkey TLR7 in complex with IMDQ and UUUUUUX-RAY DIFFRACTION2.54
464ALP|1|EThe Lin28b Cold shock domain in complex with hexauridineX-RAY DIFFRACTION1.486
477SOW|1|BLaM domain of human LARP1 in complex with UUUUUUX-RAY DIFFRACTION1.34
485SZE|1|CCrystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5AX-RAY DIFFRACTION1.53

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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