#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
215Z9W|1|RRNA (6-MER)synthetic constructEbola virus nucleoprotein-RNA complexElectron microscopy3.662018-10-24
227SOW|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
235ZSA|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
245ZSA|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
257F1M|1|SRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructMarburg virus nucleoprotein-RNA complexElectron microscopy3.162022-03-09
267F1M|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructMarburg virus nucleoprotein-RNA complexElectron microscopy3.162022-03-09
278CBW|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
287YPW|1|RRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructLloviu cuevavirus nucleoprotein-RNA complexElectron microscopy3.035662023-04-19
297EWQ|1|BRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Mumps orthorubulavirusStructure of Mumps virus nucleocapsid ringElectron microscopy3.562021-06-23
307ZNJ|1|jRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
317ZNJ|1|ORNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
326CAP|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
337ZNJ|1|JRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
347DUI|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''PyrS boundX-ray diffraction3.6262022-01-12
357ZNJ|1|oRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
367ZNJ|1|eRNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
377ZNJ|1|ERNAHomo sapiensStructure of an ALYREF-exon junction complex hexamerElectron microscopy2.462023-04-12
389FIA|1|bVulr20Toxoplasma gondiiSSU(body) structure derived from the SSU sample of the mitoribosome from T. gondii.Electron microscopy3.2962024-12-11
397DUL|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 N3''MS boundX-ray diffraction3.6262022-01-26
404NL3|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
414Y91|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
427QDZ|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
438VFT|1|wmRNAOryctolagus cuniculusTranslating 80S rabbit ribosome stalled by emetine with eEF2Electron microscopy3.362024-12-25
444Y91|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
456CAS|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
466CAR|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
474V6E|1|AWmessenger RNACrystal structure of the E. coli 70S ribosome in an intermediate state of ratchetingX-ray diffraction3.7162014-07-09
481N33|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
496JC3|1|NpolyUEscherichia coliThe Cryo-EM structure of nucleoprotein-RNA complex of Newcastle disease virusElectron microscopy4.862019-08-07
507NSJ|1|AXmRNASus scrofa55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*)Electron microscopy3.962021-06-02
514NL3|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
523PF5|1|Shexaribouracil (rU6)Crystal structure of Bs-CspB in complex with rU6X-ray diffraction1.6812011-09-21
537OZR|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
541N34|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
558R08|1|Z1oligo 1Homo sapiensCryo-EM structure of the cross-exon pre-B+AMPPNP complexElectron microscopy6.152024-05-22
5628XB|1|1RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')Homo sapiensCryo-EM structure of the human UAP56-RNA - LENG8-PCID2-SEM1 complexElectron microscopy6.262026-06-24
577YR8|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
583J9B|1|LRNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')synthetic constructElectron cryo-microscopy of an RNA polymeraseElectron microscopy4.352015-02-18
591ML5|1|CA- AND P-SITE MESSENGER RNA CODONSEscherichia coliStructure of the E. coli ribosomal termination complex with release factor 2Electron microscopy1462003-01-14
606PPN|1|AMimic of unprocessed U6 snRNAsynthetic constructStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-ray diffraction1.9152020-06-17
616PPN|1|IMimic of unprocessed U6 snRNAsynthetic constructStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-ray diffraction1.9152020-06-17
627DUK|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 N1,3''MS boundX-ray diffraction3.662022-01-12
637DUG|1|YRNA (5'-R(UPUPUPUPUPU)-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''TFMS boundX-ray diffraction3.7562022-01-12
647DUH|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
657DUJ|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 N1,3''Bz boundX-ray diffraction3.7562022-01-12

Release history

Release4.45
Date2026-06-24

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This classParent classesRelease idIntersectionAdded to this classOnly in parent

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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
21ML5|1|CStructure of the E. coli ribosomal termination complex with release factor 2ELECTRON MICROSCOPY146
33O8C|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION26
43PF5|1|SCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.681
52HYI|1|FStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
63EX7|1|JThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
73EX7|1|FThe crystal structure of EJC in its transition stateX-RAY DIFFRACTION2.36
83PEW|1|BS. cerevisiae Dbp5 L327V bound to RNA and ADP BeF3X-RAY DIFFRACTION1.56
95ELX|1|BS. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3X-RAY DIFFRACTION1.816
103PEY|1|BS. cerevisiae Dbp5 bound to RNA and ADP BeF3X-RAY DIFFRACTION1.46
112HYI|1|LStructure of the human exon junction complex with a trapped DEAD-box helicase bound to RNAX-RAY DIFFRACTION2.36
127ZNJ|1|OStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
137ZNJ|1|jStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
147ZNJ|1|eStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
157ZNJ|1|EStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
167ZNJ|1|oStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
177ZNJ|1|JStructure of an ALYREF-exon junction complex hexamerELECTRON MICROSCOPY2.46
1828XB|1|1Cryo-EM structure of the human UAP56-RNA - LENG8-PCID2-SEM1 complexELECTRON MICROSCOPY6.26
191N34|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
206CAR|1|YSerial Femtosecond X-ray Crystal Structure of 30S ribosomal subunit from Thermus thermophilus in complex with SisomicinX-RAY DIFFRACTION3.46
217DUK|1|YCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''MS boundX-RAY DIFFRACTION3.66
227DUL|1|YCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N3''MS boundX-RAY DIFFRACTION3.626
237DUJ|1|YCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1,3''Bz boundX-RAY DIFFRACTION3.756
247DUI|1|YCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''PyrS boundX-RAY DIFFRACTION3.626
257DUG|1|YCrystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with mRNA and cognate transfer RNA anticodon stem-loop and sisomicin derivative N1''TFMS boundX-RAY DIFFRACTION3.756
267DUH|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
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
291N33|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
305BTE|1|CCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.46
315BTE|1|DCrystal structure of Ashbya gossypii Rai1 in complex with pU(S)6-Mn2+X-RAY DIFFRACTION2.46
329FIA|1|bVSSU(body) structure derived from the SSU sample of the mitoribosome from T. gondii.ELECTRON MICROSCOPY3.296
336WRE|1|DCrystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ionX-RAY DIFFRACTION25
347QDZ|1|E80S-bound human SKI complex in the closed stateELECTRON MICROSCOPY3.66
353J9B|1|LElectron cryo-microscopy of an RNA polymeraseELECTRON MICROSCOPY4.35
363O8R|1|CVisualizing ATP-dependent RNA Translocation by the NS3 Helicase from HCVX-RAY DIFFRACTION2.36
373PF5|1|RCrystal structure of Bs-CspB in complex with rU6X-RAY DIFFRACTION1.685
387YPW|1|RLloviu cuevavirus nucleoprotein-RNA complexELECTRON MICROSCOPY3.03566
395Z9W|1|REbola virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.66
407OZR|1|NSubtomogram average of authentic mumps virus nucleocapsid from HeLa cell lysate of long helical pitchELECTRON MICROSCOPY4.56
417F1M|1|SMarburg virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.16
427YR8|1|RLloviu cuevavirus nucleoprotein(1-450 residues)-RNA complexELECTRON MICROSCOPY3.26
437F1M|1|RMarburg virus nucleoprotein-RNA complexELECTRON MICROSCOPY3.16
446M7D|1|BStructure of ncleoprotein of sendai virusELECTRON MICROSCOPY2.96
457EXA|1|BStructure of mumps virus nucleoprotein without C-armELECTRON MICROSCOPY2.96
467EWQ|1|BStructure of Mumps virus nucleocapsid ringELECTRON MICROSCOPY3.56
478CBW|1|1CryoEM structure of the Hendra henipavirus nucleocapsid sauronoid assembly monomerELECTRON MICROSCOPY3.4856
486JC3|1|NThe Cryo-EM structure of nucleoprotein-RNA complex of Newcastle disease virusELECTRON MICROSCOPY4.86
498RDV|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
508VFT|1|wTranslating 80S rabbit ribosome stalled by emetine with eEF2ELECTRON MICROSCOPY3.36
517NSJ|1|AX55S mammalian mitochondrial ribosome with tRNA(P/P) and tRNA(E*)ELECTRON MICROSCOPY3.96
524V6E|1|AWCrystal structure of the E. coli 70S ribosome in an intermediate state of ratchetingX-RAY DIFFRACTION3.716
536G2K|1|RStructure of HuR RRM3 in complex with RNA (UUUUUU)X-RAY DIFFRACTION2.016
546PPN|1|AStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-RAY DIFFRACTION1.915
556PPN|1|IStructure of S. pombe Lsm2-8 with unprocessed U6 snRNAX-RAY DIFFRACTION1.915
564Y91|1|NCrystal Structure of a Thermotoga maritima Hfq homologX-RAY DIFFRACTION2.666
574Y91|1|OCrystal Structure of a Thermotoga maritima Hfq homologX-RAY DIFFRACTION2.666
584NL3|1|RCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-RAY DIFFRACTION3.16
594NL3|1|ZCrystal Structure of Listeria monocytogenes Hfq in complex with U6 RNAX-RAY DIFFRACTION3.16
605ZSA|1|DCrystal structure of monkey TLR7 in complex with IMDQ and UUUUUUX-RAY DIFFRACTION2.54
615ZSA|1|CCrystal structure of monkey TLR7 in complex with IMDQ and UUUUUUX-RAY DIFFRACTION2.54
624ALP|1|EThe Lin28b Cold shock domain in complex with hexauridineX-RAY DIFFRACTION1.486
636I0U|1|BCrystal structure of DmTailor in complex with U6 RNAX-RAY DIFFRACTION24
648R08|1|Z1Cryo-EM structure of the cross-exon pre-B+AMPPNP complexELECTRON MICROSCOPY6.15
657SOW|1|BLaM domain of human LARP1 in complex with UUUUUUX-RAY DIFFRACTION1.34

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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