RNA 3D Hub //

Equivalence class NR_all_83098.7 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
18XSX|1|CC (rep)Transfer RNAE-tRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2Electron microscopy2.4752024-07-10
26ZP4|1|1Transfer RNAtRNAHomo sapiensEukaryaRF00005SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2Electron microscopy2.9752020-07-29
38PPL|1|IwTransfer RNAMet-tRNAi(Met)Homo sapiensEukaryaRF00005MERS-CoV Nsp1 bound to the human 43S pre-initiation complexElectron microscopy2.65752023-10-18
49YQ1|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 3, Structure IcElectron microscopy2.9742025-12-17
59YQ0|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 2, Structure IbElectron microscopy2.9742025-12-17
68K2C|1|CCTransfer RNAtRNA-MetHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with TigecyclineElectron microscopy2.4752024-07-10
77QVP|1|B5Transfer RNAmRNA, tRNA P/EHomo sapiensEukaryaRF00005Human collided disome (di-ribosome) stalled on XBP1 mRNAElectron microscopy3752022-10-12
88PJ5|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5)Electron microscopy2.9752024-08-14
99KRP|1|zyTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3Electron microscopy3.2752025-12-03
107A09|1|fTransfer RNAtRNAHomo sapiensEukaryaRF00005Structure of a human ABCE1-bound 43S pre-initiation complex - State IIIElectron microscopy3.5752020-10-14
118PJ6|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway)Electron microscopy2.9732024-08-14
129YPO|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaElectron microscopy3742025-12-17
136Y57|1|B4Transfer RNAmRNA, P/E tRNAHomo sapiensEukaryaRF00005Structure of human ribosome in hybrid-PRE stateElectron microscopy3.5752020-04-15
148XSZ|1|CCTransfer RNAtRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAElectron microscopy3.2752024-07-10
159KN6|1|zyTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A, eIF5B, and eIF3Electron microscopy3.3752025-12-03
169YPS|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbElectron microscopy3742025-12-17
179YPT|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcElectron microscopy3.1742025-12-17
188PJ4|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex after eIF5 release (48S-4)Electron microscopy3.2752024-08-14
199YPV|1|13Transfer RNAMet-tRNA, MF mRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdElectron microscopy3742025-12-17
208PJ1|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex in open codon scanning state (48S-1)Electron microscopy3.4752024-08-14
214UG0|1|S6Transfer RNAHUMAN INITIATOR MET-TRNA-IHomo sapiensEukaryaRF00005STRUCTURE OF THE HUMAN 80S RIBOSOMEElectron microscopy3.6752015-06-10
228PJ2|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2)Electron microscopy3.4752024-08-14
239YQ1|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 3, Structure IcElectron microscopy2.9742025-12-17
249YQ0|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005Vacant ribosome with P-site tRNA, substate 2, Structure IbElectron microscopy2.9742025-12-17
257TQL|1|3Transfer RNAHuman Met-tRNAiMetHomo sapiensEukaryaRF00005CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.Electron microscopy3.4752022-04-27
268PJ3|1|wTransfer RNAInitiator Met-tRNA-iHomo sapiensEukaryaRF00005Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3)Electron microscopy3.7752024-08-14
279YPV|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdElectron microscopy3742025-12-17
285T2C|1|AnTransfer RNAtRNAHomo sapiensEukaryaRF00005CryoEM structure of the human ribosome at 3.6 Angstrom resolutionElectron microscopy3.6752017-01-25
299YPS|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbElectron microscopy3742025-12-17
309YPO|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaElectron microscopy3742025-12-17
319YPT|1|11Transfer RNAMet-tRNAHomo sapiensEukaryaRF00005GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcElectron microscopy3.1742025-12-17
328XSZ|1|CDTransfer RNAtRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAElectron microscopy3.2752024-07-10
338XSY|1|CCTransfer RNAE-tRNAHomo sapiensEukaryaRF00005Cryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled)Electron microscopy3692024-07-10
346FEC|1|NTransfer RNAMessenger RNA (26-MER), Transfer RNA (75-MER)Homo sapiensEukaryaRF00005Human cap-dependent 48S pre-initiation complexElectron microscopy6.3752018-03-14
354V6X|1|BCTransfer RNAE-tRNAHomo sapiensEukaryaRF00005Structure of the human 80S ribosomeElectron microscopy5752014-07-09
364KZZ|1|jTransfer RNAinitiator Met-RNA-i, mRNAHomo sapiensEukaryaRF00005Rabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1AX-ray diffraction7.03752013-07-24
376QZP|1|S6Transfer RNAE site tRNA (75-MER)Homo sapiensEukaryaRF00005High-resolution cryo-EM structure of the human 80S ribosomeElectron microscopy2.9752019-04-24

Release history

Release4.18
Date2025-12-17

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

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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
18XSZ|1|CDCryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAELECTRON MICROSCOPY3.275
29YPS|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY374
39YPT|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcELECTRON MICROSCOPY3.174
49YPV|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY374
59YQ1|1|13Vacant ribosome with P-site tRNA, substate 3, Structure IcELECTRON MICROSCOPY2.974
69YQ0|1|13Vacant ribosome with P-site tRNA, substate 2, Structure IbELECTRON MICROSCOPY2.974
79YPO|1|13GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY374
84KZZ|1|jRabbit 40S ribosomal subunit in complex with mRNA, initiator tRNA and eIF1AX-RAY DIFFRACTION7.0375
96QZP|1|S6High-resolution cryo-EM structure of the human 80S ribosomeELECTRON MICROSCOPY2.975
105T2C|1|AnCryoEM structure of the human ribosome at 3.6 Angstrom resolutionELECTRON MICROSCOPY3.675
114UG0|1|S6STRUCTURE OF THE HUMAN 80S RIBOSOMEELECTRON MICROSCOPY3.675
129YQ1|1|11Vacant ribosome with P-site tRNA, substate 3, Structure IcELECTRON MICROSCOPY2.974
139YPV|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIdELECTRON MICROSCOPY374
149YPT|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIcELECTRON MICROSCOPY3.174
159YPO|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIaELECTRON MICROSCOPY374
169YPS|1|11GTPBP1*GCP*Phe-tRNA*ribosome in the open state, Structure IIbELECTRON MICROSCOPY374
179YQ0|1|11Vacant ribosome with P-site tRNA, substate 2, Structure IbELECTRON MICROSCOPY2.974
188XSY|1|CCCryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled)ELECTRON MICROSCOPY369
198K2C|1|CCCryo-EM structure of the human 80S ribosome with TigecyclineELECTRON MICROSCOPY2.475
208XSX|1|CCCryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2ELECTRON MICROSCOPY2.475
218XSZ|1|CCCryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNAELECTRON MICROSCOPY3.275
226Y57|1|B4Structure of human ribosome in hybrid-PRE stateELECTRON MICROSCOPY3.575
237QVP|1|B5Human collided disome (di-ribosome) stalled on XBP1 mRNAELECTRON MICROSCOPY375
244V6X|1|BCStructure of the human 80S ribosomeELECTRON MICROSCOPY575
256FEC|1|NHuman cap-dependent 48S pre-initiation complexELECTRON MICROSCOPY6.375
268PJ1|1|wStructure of human 48S translation initiation complex in open codon scanning state (48S-1)ELECTRON MICROSCOPY3.475
278PPL|1|IwMERS-CoV Nsp1 bound to the human 43S pre-initiation complexELECTRON MICROSCOPY2.6575
286ZP4|1|1SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2ELECTRON MICROSCOPY2.975
297A09|1|fStructure of a human ABCE1-bound 43S pre-initiation complex - State IIIELECTRON MICROSCOPY3.575
308PJ6|1|wStructure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway)ELECTRON MICROSCOPY2.973
318PJ2|1|wStructure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2)ELECTRON MICROSCOPY3.475
328PJ5|1|wStructure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5)ELECTRON MICROSCOPY2.975
338PJ4|1|wStructure of human 48S translation initiation complex after eIF5 release (48S-4)ELECTRON MICROSCOPY3.275
348PJ3|1|wStructure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3)ELECTRON MICROSCOPY3.775
359KN6|1|zyStructure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A, eIF5B, and eIF3ELECTRON MICROSCOPY3.375
369KRP|1|zyStructure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3ELECTRON MICROSCOPY3.275
377TQL|1|3CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B.ELECTRON MICROSCOPY3.475

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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