RNA 3D Hub //

Equivalence class NR_20.0_38961.6 Current

Showing 1 to 9 of 9 entries
#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
17OSM|1|ASIT (rep)Transfer RNAMRNA, PHE tRNASaccharomyces cerevisiaeEukaryaRF00005Intermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligandsX-ray diffraction3762021-12-08
27ZUX|1|6Transfer RNAA/P tRNASaccharomyces cerevisiaeEukaryaRF00005Collided ribosome in a disome unit from S. cerevisiaeElectron microscopy2.5762023-02-22
36ZVI|1|dTransfer RNAA/P-site tRNA, mRNASaccharomyces cerevisiaeEukaryaRF00005Mbf1-ribosome complexElectron microscopy3762020-09-09
46SV4|1|nbTransfer RNAtRNA (A/P)Saccharomyces cerevisiaeEukaryaRF00005The cryo-EM structure of SDD1-stalled collided trisome.Electron microscopy3.3762020-03-04
56SV4|1|ncTransfer RNAtRNA (A/P)Saccharomyces cerevisiaeEukaryaRF00005The cryo-EM structure of SDD1-stalled collided trisome.Electron microscopy3.3762020-03-04
66UZ7|1|3Transfer RNARNA (76-MER)Saccharomyces cerevisiaeEukaryaRF00005K.lactis 80S ribosome with p/PE tRNA and eIF5BElectron microscopy3.6762020-01-15
74V8Y|1|CWTransfer RNAEUKARYOTIC RIBOSOMAL P_E TRNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation ComplexElectron microscopy4.3742014-07-09
86I7O|1|nbTransfer RNAA/P hybrid tRNASaccharomyces cerevisiaeEukaryaRF00005The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.Electron microscopy5.3762019-01-16
94V8Z|1|CWTransfer RNAEUKARYOTIC RIBOSOMAL PI TRNASaccharomyces cerevisiaeEukaryaRF00005Cryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation ComplexElectron microscopy6.6762014-07-09

Release history

Release3.3823.3833.3843.3853.3863.3873.3883.3893.3903.3913.3923.393
Date2025-04-092025-04-162025-04-232025-04-302025-05-072025-05-142025-05-212025-05-282025-06-042025-06-112025-06-182025-06-25

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.

Showing 1 to 9 of 9 entries
#SViewPDBTitleMethodResolution#NTs
14V8Z|1|CWCryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation ComplexELECTRON MICROSCOPY6.676
27OSM|1|ASITIntermediate translocation complex of 80 S.cerevisiae ribosome with eEF2 and ligandsX-RAY DIFFRACTION376
36ZVI|1|dMbf1-ribosome complexELECTRON MICROSCOPY376
46SV4|1|ncThe cryo-EM structure of SDD1-stalled collided trisome.ELECTRON MICROSCOPY3.376
56SV4|1|nbThe cryo-EM structure of SDD1-stalled collided trisome.ELECTRON MICROSCOPY3.376
66I7O|1|nbThe structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.ELECTRON MICROSCOPY5.376
77ZUX|1|6Collided ribosome in a disome unit from S. cerevisiaeELECTRON MICROSCOPY2.576
84V8Y|1|CWCryo-EM reconstruction of the 80S-eIF5B-Met-itRNAMet Eukaryotic Translation Initiation ComplexELECTRON MICROSCOPY4.374
96UZ7|1|3K.lactis 80S ribosome with p/PE tRNA and eIF5BELECTRON MICROSCOPY3.676

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.

4V8Z|1|CW:4V8Z|1|CW = 04V8Z|1|CW:7OSM|1|ASIT = 0.44164V8Z|1|CW:6ZVI|1|d = 0.52174V8Z|1|CW:6SV4|1|nc = 0.49734V8Z|1|CW:6SV4|1|nb = 0.50254V8Z|1|CW:6I7O|1|nb = 0.50184V8Z|1|CW:7ZUX|1|6 = 0.52814V8Z|1|CW:4V8Y|1|CW = 0.49604V8Z|1|CW:6UZ7|1|3 = 0.57927OSM|1|ASIT:4V8Z|1|CW = 0.44167OSM|1|ASIT:7OSM|1|ASIT = 07OSM|1|ASIT:6ZVI|1|d = 0.36547OSM|1|ASIT:6SV4|1|nc = 0.35557OSM|1|ASIT:6SV4|1|nb = 0.35557OSM|1|ASIT:6I7O|1|nb = 0.36167OSM|1|ASIT:7ZUX|1|6 = 0.40137OSM|1|ASIT:4V8Y|1|CW = 0.48687OSM|1|ASIT:6UZ7|1|3 = 0.50026ZVI|1|d:4V8Z|1|CW = 0.52176ZVI|1|d:7OSM|1|ASIT = 0.36546ZVI|1|d:6ZVI|1|d = 06ZVI|1|d:6SV4|1|nc = 0.16316ZVI|1|d:6SV4|1|nb = 0.16176ZVI|1|d:6I7O|1|nb = 0.16516ZVI|1|d:7ZUX|1|6 = 0.27486ZVI|1|d:4V8Y|1|CW = 0.49316ZVI|1|d:6UZ7|1|3 not available6SV4|1|nc:4V8Z|1|CW = 0.49736SV4|1|nc:7OSM|1|ASIT = 0.35556SV4|1|nc:6ZVI|1|d = 0.16316SV4|1|nc:6SV4|1|nc = 06SV4|1|nc:6SV4|1|nb = 0.06366SV4|1|nc:6I7O|1|nb = 0.08556SV4|1|nc:7ZUX|1|6 = 0.24776SV4|1|nc:4V8Y|1|CW = 0.43636SV4|1|nc:6UZ7|1|3 not available6SV4|1|nb:4V8Z|1|CW = 0.50256SV4|1|nb:7OSM|1|ASIT = 0.35556SV4|1|nb:6ZVI|1|d = 0.16176SV4|1|nb:6SV4|1|nc = 0.06366SV4|1|nb:6SV4|1|nb = 06SV4|1|nb:6I7O|1|nb = 0.08416SV4|1|nb:7ZUX|1|6 = 0.24496SV4|1|nb:4V8Y|1|CW = 0.43996SV4|1|nb:6UZ7|1|3 not available6I7O|1|nb:4V8Z|1|CW = 0.50186I7O|1|nb:7OSM|1|ASIT = 0.36166I7O|1|nb:6ZVI|1|d = 0.16516I7O|1|nb:6SV4|1|nc = 0.08556I7O|1|nb:6SV4|1|nb = 0.08416I7O|1|nb:6I7O|1|nb = 06I7O|1|nb:7ZUX|1|6 = 0.24466I7O|1|nb:4V8Y|1|CW = 0.43796I7O|1|nb:6UZ7|1|3 not available7ZUX|1|6:4V8Z|1|CW = 0.52817ZUX|1|6:7OSM|1|ASIT = 0.40137ZUX|1|6:6ZVI|1|d = 0.27487ZUX|1|6:6SV4|1|nc = 0.24777ZUX|1|6:6SV4|1|nb = 0.24497ZUX|1|6:6I7O|1|nb = 0.24467ZUX|1|6:7ZUX|1|6 = 07ZUX|1|6:4V8Y|1|CW = 0.47987ZUX|1|6:6UZ7|1|3 not available4V8Y|1|CW:4V8Z|1|CW = 0.49604V8Y|1|CW:7OSM|1|ASIT = 0.48684V8Y|1|CW:6ZVI|1|d = 0.49314V8Y|1|CW:6SV4|1|nc = 0.43634V8Y|1|CW:6SV4|1|nb = 0.43994V8Y|1|CW:6I7O|1|nb = 0.43794V8Y|1|CW:7ZUX|1|6 = 0.47984V8Y|1|CW:4V8Y|1|CW = 04V8Y|1|CW:6UZ7|1|3 = 0.27166UZ7|1|3:4V8Z|1|CW = 0.57926UZ7|1|3:7OSM|1|ASIT = 0.50026UZ7|1|3:6ZVI|1|d not available6UZ7|1|3:6SV4|1|nc not available6UZ7|1|3:6SV4|1|nb not available6UZ7|1|3:6I7O|1|nb not available6UZ7|1|3:7ZUX|1|6 not available6UZ7|1|3:4V8Y|1|CW = 0.27166UZ7|1|3:6UZ7|1|3 = 04V8Z|1|CW7OSM|1|ASIT6ZVI|1|d6SV4|1|nc6SV4|1|nb6I7O|1|nb7ZUX|1|64V8Y|1|CW6UZ7|1|3Discrepancy0.000.100.200.300.400.50

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