RNA 3D Hub //

Equivalence class NR_2.5_46995.72 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
19TV2|1|S2 (rep)Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF0196080S ribosomes from primary B-cells infected with delta v-snoRNA1 EBVElectron microscopy2.114812026-07-01
29TT7|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF0196080S ribosome of WT EBV infected human B-cellsElectron microscopy2.215032026-07-22
38GLP|1|S2Small 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
48QOI|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
59SPF|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
68YOO|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Cryo-EM structure of the human 80S ribosome with 100 um TigecyclineElectron microscopy217192024-07-10
79O3W|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Human 80S ribosome bound to IDB-001 stalled on MYC nascent chainElectron microscopy1.916722026-03-04
89O3V|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Human 80S ribosome stalled on MYC nascent chainElectron microscopy2.216722026-03-04
99S3D|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NAC bound human RNC with 58 amino acid ARF1-linkerElectron microscopy2.3217132026-02-18
109C3H|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
119S3B|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1Electron microscopy2.3817132026-02-18
128G5Y|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)Electron microscopy2.2916802023-04-19
139S3C|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2Electron microscopy2.4217132026-02-18
149QLO|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with full length ARF1 - State 1Electron microscopy2.4717132026-02-18
159I2D|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960NMT1-NAC bound human RNC with 10 amino acid ARF1-linkerElectron microscopy2.1917132026-02-04
169SPI|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
178YOP|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Cryo-EM structure of the human 80S ribosome with 4 um TigecyclineElectron microscopy2.217402024-07-10
189O3Y|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chainElectron microscopy2.216722026-03-04
199RUC|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960WT-HEK 80S ribosome bound to H2B mRNA (WT-H2B)Electron microscopy2.514552026-05-13
209PBE|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960In situ human 80S ribosome (composite map)Electron microscopy2.1917402025-12-24
218K2C|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Cryo-EM structure of the human 80S ribosome with TigecyclineElectron microscopy2.417402024-07-10
229P8B|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960In situ human eEF1A-A/T-P-E state 80S ribosomeElectron microscopy2.4817402025-12-24
239RPV|1|S3Small subunit ribosomal RNA18S rRNA of the stalled 80SHomo sapiensEukaryaRF01960Structure of the ZAK-bound human disomeElectron microscopy2.3516722025-12-10
247XNY|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
258XSX|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
269RPV|1|S2Small subunit ribosomal RNA18S rRNA of the collided 80SHomo sapiensEukaryaRF01960Structure of the ZAK-bound human disomeElectron microscopy2.3517562025-12-10
277R4X|1|2Small subunit ribosomal RNA18S ribosomal RNAHomo sapiensEukaryaRF01960Cryo-EM reconstruction of the human 40S ribosomal subunit - Full mapElectron microscopy2.1516462023-02-22
288JDJ|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
299PKD|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960In situ CHX and HHT treated 80S consensus ribosomeElectron microscopy2.4217402026-07-15
308JDL|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
319MNC|1|S2Small subunit ribosomal RNA18S rRNAHomo sapiensEukaryaRF01960Human 80S ribosome bound to small molecule SW393071Electron microscopy2.3316352026-06-24
328JDK|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

Release history

Release4.49
Date2026-07-22

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
19PKD|1|S2In situ CHX and HHT treated 80S consensus ribosomeELECTRON MICROSCOPY2.421740
29RUC|1|S2WT-HEK 80S ribosome bound to H2B mRNA (WT-H2B)ELECTRON MICROSCOPY2.51455
39S3B|1|S2NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1ELECTRON MICROSCOPY2.381713
49S3C|1|S2NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2ELECTRON MICROSCOPY2.421713
59S3D|1|S2NAC bound human RNC with 58 amino acid ARF1-linkerELECTRON MICROSCOPY2.321713
69I2D|1|S2NMT1-NAC bound human RNC with 10 amino acid ARF1-linkerELECTRON MICROSCOPY2.191713
79QLO|1|S2NMT1-NAC bound human RNC with full length ARF1 - State 1ELECTRON MICROSCOPY2.471713
89TV2|1|S280S ribosomes from primary B-cells infected with delta v-snoRNA1 EBVELECTRON MICROSCOPY2.11481
99C3H|1|S2Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site.ELECTRON MICROSCOPY21660
109MNC|1|S2Human 80S ribosome bound to small molecule SW393071ELECTRON MICROSCOPY2.331635
117XNY|1|S2High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cellsELECTRON MICROSCOPY2.51740
128YOP|1|S2Cryo-EM structure of the human 80S ribosome with 4 um TigecyclineELECTRON MICROSCOPY2.21740
138K2C|1|S2Cryo-EM structure of the human 80S ribosome with TigecyclineELECTRON MICROSCOPY2.41740
148YOO|1|S2Cryo-EM structure of the human 80S ribosome with 100 um TigecyclineELECTRON MICROSCOPY21719
159PBE|1|S2In situ human 80S ribosome (composite map)ELECTRON MICROSCOPY2.191740
169P8B|1|S2In situ human eEF1A-A/T-P-E state 80S ribosomeELECTRON MICROSCOPY2.481740
178QOI|1|S2Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNAELECTRON MICROSCOPY1.91740
188G5Y|1|S2mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state)ELECTRON MICROSCOPY2.291680
198GLP|1|S2mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure)ELECTRON MICROSCOPY1.671672
209RPV|1|S3Structure of the ZAK-bound human disomeELECTRON MICROSCOPY2.351672
219O3W|1|S2Human 80S ribosome bound to IDB-001 stalled on MYC nascent chainELECTRON MICROSCOPY1.91672
229O3Y|1|S2Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chainELECTRON MICROSCOPY2.21672
239O3V|1|S2Human 80S ribosome stalled on MYC nascent chainELECTRON MICROSCOPY2.21672
249SPF|1|S2CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINEELECTRON MICROSCOPY2.41619
259RPV|1|S2Structure of the ZAK-bound human disomeELECTRON MICROSCOPY2.351756
269SPI|1|S2CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINEELECTRON MICROSCOPY2.41562
278JDK|1|wStructure of the Human cytoplasmic Ribosome with human tRNA Asp(ManQ34) and mRNA(GAU)ELECTRON MICROSCOPY2.261634
288JDJ|1|wStructure of the Human cytoplasmic Ribosome with human tRNA Asp(Q34) and mRNA(GAU)ELECTRON MICROSCOPY2.51634
298JDL|1|wStructure of the Human cytoplasmic Ribosome with human tRNA Tyr(GalQ34) and mRNA(UAU) (non-rotated state)ELECTRON MICROSCOPY2.421634
309TT7|1|S280S ribosome of WT EBV infected human B-cellsELECTRON MICROSCOPY2.21503
317R4X|1|2Cryo-EM reconstruction of the human 40S ribosomal subunit - Full mapELECTRON MICROSCOPY2.151646
328XSX|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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