RNA 3D Hub //

Equivalence class NR_20.0_74924.25 Obsolete

#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
52HYI|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
66G2K|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
72HYI|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
83EX7|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
95SZE|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
103EX7|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
113O8C|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
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
133PF5|1|Rhexaribouracil (rU6)Crystal structure of Bs-CspB in complex with rU6X-ray diffraction1.6852011-09-21
145BTE|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
156WRE|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
167SOW|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
176I0U|1|BRNA (5'-R(*UP*UP*UP*U)-3')Drosophila melanogasterCrystal structure of DmTailor in complex with U6 RNAX-ray diffraction242018-12-05
185ZSA|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
195ZSA|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
203O8R|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
214NL3|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
224Y91|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
234Y91|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
244NL3|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
251N34|1|ZA-SITE MESSENGER RNA FRAGMENTThermus thermophilusStructure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon positionX-ray diffraction3.842002-11-29
263PF5|1|Shexaribouracil (rU6)Crystal structure of Bs-CspB in complex with rU6X-ray diffraction1.6812011-09-21
276PPN|1|AMimic of unprocessed U6 snRNAsynthetic constructStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-ray diffraction1.9152020-06-17
286PPN|1|IMimic of unprocessed U6 snRNAsynthetic constructStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-ray diffraction1.9152020-06-17
297DUH|1|YRNA (5'-R(*UP*UP*UP*UP*UP*U)-3')Thermus thermophilusCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''AC boundX-ray diffraction3.7562022-01-26
307ZNJ|1|ERNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
317ZNJ|1|JRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
327ZNJ|1|ORNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
337ZNJ|1|eRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
347ZNJ|1|jRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
357ZNJ|1|oRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
368RDV|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
376M7D|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructStructure of ncleoprotein of sendai virusElectron microscopy2.962021-03-24
387EXA|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
397YPW|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructLloviu cuevavirus nucleoprotein-RNA complexElectron microscopy3.035662023-04-19
407F1M|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructMarburg virus nucleoprotein-RNA complexElectron microscopy3.162022-03-09
417F1M|1|SRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructMarburg virus nucleoprotein-RNA complexElectron microscopy3.162022-03-09
427YR8|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
438CBW|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
447EWQ|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Mumps orthorubulavirusStructure of Mumps virus nucleocapsid ringElectron microscopy3.562021-06-23
457QDZ|1|ERNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Homo sapiens80S-bound human SKI complex in the closed stateElectron microscopy3.662022-02-09
465Z9W|1|RRNA (6-MER)synthetic constructEbola virus nucleoprotein-RNA complexElectron microscopy3.662018-10-24
477NSJ|1|AXmRNASus scrofa55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*)Electron microscopy3.962021-06-02
486JC3|1|NpolyUEscherichia coliThe Cryo-EM structure of nucleoprotein-RNA complex of Newcastle disease virusElectron microscopy4.862019-08-07
497OZR|1|NRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Mumps virus genotype ASubtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitchElectron microscopy4.562023-03-01
508R08|1|Z1oligo 1Homo sapiensCryo-EM structure of the cross-exon pre-B+AMPPNP complexElectron microscopy6.152024-05-22

Release history

Release3.3493.3503.3513.3523.3533.3543.3553.3563.3573.3583.3593.3603.3613.3623.3633.364
Date2024-08-212024-08-282024-09-042024-09-112024-09-182024-09-252024-10-022024-10-092024-10-162024-10-232024-10-302024-11-062024-11-132024-11-202024-11-272024-12-04

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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
15SZE|1|CCrystal structure of Aquifex aeolicus Hfq-RNA complex at 1.5AX-RAY DIFFRACTION1.53
27SOW|1|BLaM domain of human LARP1 in complex with UUUUUUX-RAY DIFFRACTION1.34
35BTE|1|DCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.46
45BTE|1|CCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.46
57YPW|1|RLloviu cuevavirus nucleoprotein-RNA complexELECTRON MICROSCOPY3.03566
65Z9W|1|REbola virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.66
77OZR|1|NSubtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitchELECTRON MICROSCOPY4.56
86JC3|1|NThe Cryo-EM structure of nucleoprotein-RNA complex of Newcastle disease virusELECTRON MICROSCOPY4.86
98CBW|1|1CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid assembly monomerELECTRON MICROSCOPY3.4856
107EWQ|1|BStructure of Mumps virus nucleocapsid ringELECTRON MICROSCOPY3.56
116M7D|1|BStructure of ncleoprotein of sendai virusELECTRON MICROSCOPY2.96
127EXA|1|BStructure of mumps virus nucleoprotein without C-armELECTRON MICROSCOPY2.96
137F1M|1|SMarburg virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.16
147F1M|1|RMarburg virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.16
157YR8|1|RLloviu cuevavirus nucleoprotein(1-450 residues)-RNA complexELECTRON MICROSCOPY3.26
163O8R|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION2.36
176WRE|1|DCrystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ionX-RAY DIFFRACTION25
187QDZ|1|E80S-bound human SKI complex in the closed stateELECTRON MICROSCOPY3.66
195ELX|1|BS. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3X-RAY DIFFRACTION1.816
203PEY|1|BS. cerevisiae Dbp5 bound to RNA and ADP BeF3X-RAY DIFFRACTION1.46
213PEW|1|BS. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3X-RAY DIFFRACTION1.56
223EX7|1|FThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
232HYI|1|LStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
242HYI|1|FStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
253EX7|1|JThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
267ZNJ|1|OStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
277ZNJ|1|jStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
287ZNJ|1|eStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
297ZNJ|1|JStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
307ZNJ|1|oStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
317ZNJ|1|EStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
321N34|1|ZStructure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon positionX-RAY DIFFRACTION3.84
337DUH|1|YCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''AC boundX-RAY DIFFRACTION3.756
343PF5|1|RCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.685
358RDV|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
367NSJ|1|AX55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*)ELECTRON MICROSCOPY3.96
376G2K|1|RStructure of HuR RRM3 in complex with RNA (UUUUUU)X-RAY DIFFRACTION2.016
386PPN|1|AStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-RAY DIFFRACTION1.915
396PPN|1|IStructure 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|ZCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-RAY DIFFRACTION3.16
434NL3|1|RCrystal 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
476I0U|1|BCrystal structure of DmTailor in complex with U6 RNAX-RAY DIFFRACTION24
488R08|1|Z1Cryo-EM structure of the cross-exon pre-B+AMPPNP complexELECTRON MICROSCOPY6.15
493O8C|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION26
503PF5|1|SCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.681

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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