RNA 3D Hub //

Equivalence class NR_2.5_46995.63 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
18GLP|1|S2 (rep)Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)Electron microscopy1.6716722023-04-19
28QOI|1|S2Small subunit ribosomal RNA18S rRNA (1740-MER)Homo sapiensEukaryaRF01960Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNAElectron microscopy1.917402024-06-12
39SPF|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINEElectron microscopy2.416192026-01-21
48YOO|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Cryo-EM structure of the human 80S ribosome with 100 um TigecyclineElectron microscopy217192024-07-10
59O3W|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Human 80S ribosome bound to IDB-001 stalled on MYC nascent chainElectron microscopy1.916722026-03-04
69O3V|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Human 80S ribosome stalled on MYC nascent chainElectron microscopy2.216722026-03-04
79S3D|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NAC bound human RNC with 58 amino acid ARF1-linkerElectron microscopy2.3217132026-02-18
89C3H|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.Electron microscopy216602024-12-04
99S3B|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1Electron microscopy2.3817132026-02-18
108G5Y|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)Electron microscopy2.2916802023-04-19
119S3C|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2Electron microscopy2.4217132026-02-18
129QLO|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with full length ARF1 - State 1Electron microscopy2.4717132026-02-18
139I2D|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with 10 amino acid ARF1-linkerElectron microscopy2.1917132026-02-04
149SPI|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINEElectron microscopy2.415622026-01-21
158YOP|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Cryo-EM structure of the human 80S ribosome with 4 um TigecyclineElectron microscopy2.217402024-07-10
169O3Y|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chainElectron microscopy2.216722026-03-04
179PBE|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960In situ human 80S ribosome (composite map)Electron microscopy2.1917402025-12-24
188K2C|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Cryo-EM structure of the human 80S ribosome with TigecyclineElectron microscopy2.417402024-07-10
199P8B|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960In situ human eEF1A-A/T-P-E state 80S ribosomeElectron microscopy2.4817402025-12-24
209RPV|1|S3Small subunit ribosomal RNA18S rRNA of the stalled 80SHomo sapiensEukaryaRF01960Structure of the ZAK-bound human disomeElectron microscopy2.3516722025-12-10
217XNY|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cellsElectron microscopy2.517402023-04-05
228XSX|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2Electron microscopy2.417402024-07-10
239RPV|1|S2Small subunit ribosomal RNA18S rRNA of the collided 80SHomo sapiensEukaryaRF01960Structure of the ZAK-bound human disomeElectron microscopy2.3517562025-12-10
247R4X|1|2Small subunit ribosomal RNA18S ribosomal RNAHomo sapiensEukaryaRF01960Cryo-EM reconstruction of the human 40S ribosomal subunit - Full mapElectron microscopy2.1516462023-02-22
258JDJ|1|wSmall subunit ribosomal RNA18S ribosomal RNAHomo sapiensEukaryaRF01960Structure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)Electron microscopy2.516342023-12-06
268JDL|1|wSmall subunit ribosomal RNA18S ribosomal RNAHomo sapiensEukaryaRF01960Structure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)Electron microscopy2.4216342023-12-06
278JDK|1|wSmall subunit ribosomal RNA18S ribosomal RNAHomo sapiensEukaryaRF01960Structure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)Electron microscopy2.2616342023-12-06
289AZC|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960In situ human 80S ribosome (Consensus map)Electron microscopy2.1917402025-04-30

Release history

Release4.29
Date2026-03-04

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
18JDL|1|wStructure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)ELECTRON MICROSCOPY2.421634
28JDJ|1|wStructure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)ELECTRON MICROSCOPY2.51634
38JDK|1|wStructure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)ELECTRON MICROSCOPY2.261634
49SPI|1|S2CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINEELECTRON MICROSCOPY2.41562
59RPV|1|S2Structure of the ZAK-bound human disomeELECTRON MICROSCOPY2.351756
69SPF|1|S2CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINEELECTRON MICROSCOPY2.41619
79O3V|1|S2Human 80S ribosome stalled on MYC nascent chainELECTRON MICROSCOPY2.21672
89O3Y|1|S2Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chainELECTRON MICROSCOPY2.21672
99O3W|1|S2Human 80S ribosome bound to IDB-001 stalled on MYC nascent chainELECTRON MICROSCOPY1.91672
108G5Y|1|S2mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)ELECTRON MICROSCOPY2.291680
118GLP|1|S2mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)ELECTRON MICROSCOPY1.671672
129RPV|1|S3Structure of the ZAK-bound human disomeELECTRON MICROSCOPY2.351672
139C3H|1|S2Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.ELECTRON MICROSCOPY21660
147XNY|1|S2High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cellsELECTRON MICROSCOPY2.51740
158YOP|1|S2Cryo-EM structure of the human 80S ribosome with 4 um TigecyclineELECTRON MICROSCOPY2.21740
168K2C|1|S2Cryo-EM structure of the human 80S ribosome with TigecyclineELECTRON MICROSCOPY2.41740
178YOO|1|S2Cryo-EM structure of the human 80S ribosome with 100 um TigecyclineELECTRON MICROSCOPY21719
189PBE|1|S2In situ human 80S ribosome (composite map)ELECTRON MICROSCOPY2.191740
199P8B|1|S2In situ human eEF1A-A/T-P-E state 80S ribosomeELECTRON MICROSCOPY2.481740
209AZC|1|S2In situ human 80S ribosome (Consensus map)ELECTRON MICROSCOPY2.191740
218QOI|1|S2Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNAELECTRON MICROSCOPY1.91740
229S3B|1|S2NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1ELECTRON MICROSCOPY2.381713
239S3C|1|S2NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2ELECTRON MICROSCOPY2.421713
249S3D|1|S2NAC bound human RNC with 58 amino acid ARF1-linkerELECTRON MICROSCOPY2.321713
259I2D|1|S2NMT1-NAC bound human RNC with 10 amino acid ARF1-linkerELECTRON MICROSCOPY2.191713
269QLO|1|S2NMT1-NAC bound human RNC with full length ARF1 - State 1ELECTRON MICROSCOPY2.471713
277R4X|1|2Cryo-EM reconstruction of the human 40S ribosomal subunit - Full mapELECTRON MICROSCOPY2.151646
288XSX|1|S2Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2ELECTRON MICROSCOPY2.41740

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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