NR_2.5_35542.104

Members (22)
History
Heat map

#	IFE	Standardized name	Molecule	Organism	Source	Rfam	Title	Method	Res. Å	Date
1	7RQ8\|1\|1x (rep)	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.50A resolution	X-ray diffraction	2.5	2021-10-13
2	6XHW\|1\|1x	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution	X-ray diffraction	2.5	2020-12-23
3	7RQ8\|1\|2x	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.50A resolution	X-ray diffraction	2.5	2021-10-13
4	8CVK\|1\|1x	Transfer RNA	P-site Peptidyl-tRNA fMRC-NH-tRNAmet RNA-part, MF-mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution	X-ray diffraction	2.5	2022-10-19
5	6XHV\|1\|1x	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.40A resolution	X-ray diffraction	2.4	2020-12-23
6	8CVK\|1\|2x	Transfer RNA	P-site Peptidyl-tRNA fMRC-NH-tRNAmet RNA-part, MF-mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution	X-ray diffraction	2.5	2022-10-19
7	6XHW\|1\|2x	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution	X-ray diffraction	2.5	2020-12-23
8	6XHV\|1\|2x	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.40A resolution	X-ray diffraction	2.4	2020-12-23
9	4Y4P\|1\|1x	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to mRNA and A-, P- and E-site tRNAs at 2.5A resolution	X-ray diffraction	2.5	2015-03-18
10	8CVJ\|1\|1x	Transfer RNA	P-site Peptidyl-tRNA fMSEAC-NH-tRNAmet RNA-part, MF-mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution	X-ray diffraction	2.4	2022-10-19
11	8CVJ\|1\|2x	Transfer RNA	P-site Peptidyl-tRNA fMSEAC-NH-tRNAmet RNA-part, MF-mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution	X-ray diffraction	2.4	2022-10-19
12	8CVL\|1\|1x	Transfer RNA	P-site Peptidyl-tRNA fMTHSMRC-NH-tRNAmet RNA-part, MF-mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMTHSMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.30A resolution	X-ray diffraction	2.3	2022-10-19
13	4W2F\|1\|AX	Transfer RNA	E-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites	X-ray diffraction	2.4	2014-10-15
14	8CVL\|1\|2x	Transfer RNA	P-site Peptidyl-tRNA fMTHSMRC-NH-tRNAmet RNA-part, MF-mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMTHSMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.30A resolution	X-ray diffraction	2.3	2022-10-19
15	4W2F\|1\|CX	Transfer RNA	E-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites	X-ray diffraction	2.4	2014-10-15
16	4Y4P\|1\|2x	Transfer RNA	P-site tRNA, mRNA	Escherichia coli	Bacteria	RF00005	Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to mRNA and A-, P- and E-site tRNAs at 2.5A resolution	X-ray diffraction	2.5	2015-03-18
17	8B0X\|1\|Z	Transfer RNA	P-site tRNA, mRNA	Escherichia coli B	Bacteria	RF00005	Translating 70S ribosome in the unrotated state (P and E, tRNAs)	Electron microscopy	1.55	2022-11-30
18	7K00\|1\|Z	Transfer RNA	P-site tRNA-fMet, mRNA	Escherichia coli	Bacteria	RF00005	Structure of the Bacterial Ribosome at 2 Angstrom Resolution	Electron microscopy	1.98	2020-09-23
19	6XZ7\|1\|f	Transfer RNA	Deacylated tRNAi(Met)	Escherichia coli	Bacteria	RF00005	E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).	Electron microscopy	2.1	2020-07-22
20	7TOP\|1\|APTN	Transfer RNA	tRNAfMet	Escherichia coli	Bacteria	RF00005	Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20	Electron microscopy	2.4	2022-05-25
21	7ZHG\|1\|4	Transfer RNA	Met-tRNAiMet, mRNA	Pyrococcus abyssi GE5	Archaea	RF00005	High-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop	Electron microscopy	2.25	2022-06-29
22	6YSI\|1\|8+ 6YSI\|1\|6	Transfer RNA + Transfer RNA	E-site tRNA	Acinetobacter baumannii	Bacteria	RF00005 + RF00005	Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit	Electron microscopy	2.5	2020-09-16

Release history

Release	3.262	3.263	3.264	3.265	3.266
Date	2022-12-21	2022-12-28	2023-01-04	2023-01-11	2023-01-18

Parents

This class	Parent classes	Release id	Intersection	Added to this class	Only in parent
NR_2.5_35542.104	NR_2.5_35542.103	3.262	(22) 4W2F\|1\|AX, 7RQ8\|1\|2x, 7TOP\|1\|APTN, 7ZHG\|1\|4, 8B0X\|1\|Z, 8CVJ\|1\|1x, 8CVJ\|1\|2x, 8CVK\|1\|1x, 8CVK\|1\|2x, 8CVL\|1\|1x, 7RQ8\|1\|1x, 7K00\|1\|Z, 4W2F\|1\|CX, 4Y4P\|1\|1x, 4Y4P\|1\|2x, 6XHV\|1\|1x, 6XHV\|1\|2x, 6XHW\|1\|1x, 6XHW\|1\|2x, 6XZ7\|1\|f, 6YSI\|1\|8+6YSI\|1\|6, 8CVL\|1\|2x	(0)	(0)

Children

This class	Descendant classes	Release id	Intersection	Only in this class	Added to child
NR_2.5_35542.104	NR_2.5_35542.105	3.267	(22) 4W2F\|1\|AX, 7RQ8\|1\|2x, 7TOP\|1\|APTN, 7ZHG\|1\|4, 8B0X\|1\|Z, 8CVJ\|1\|1x, 8CVJ\|1\|2x, 8CVK\|1\|1x, 8CVK\|1\|2x, 8CVL\|1\|1x, 7RQ8\|1\|1x, 7K00\|1\|Z, 4W2F\|1\|CX, 4Y4P\|1\|1x, 4Y4P\|1\|2x, 6XHV\|1\|1x, 6XHV\|1\|2x, 6XHW\|1\|1x, 6XHW\|1\|2x, 6XZ7\|1\|f, 6YSI\|1\|8+6YSI\|1\|6, 8CVL\|1\|2x	(0)	(0)

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. Instances are ordered to put similar structures near each other. The colorbar ranges from 0 to the maximum observed discrepancy, up to 0.5

#S - ordering by similarity (same as in the heat map).

#S	PDB	Title	Method	Resolution	Length
1	8B0X\|1\|Z	Translating 70S ribosome in the unrotated state (P and E, tRNAs)	ELECTRON MICROSCOPY	1.55	75
2	7K00\|1\|Z	Structure of the Bacterial Ribosome at 2 Angstrom Resolution	ELECTRON MICROSCOPY	1.98	76
3	6XZ7\|1\|f	E. coli 50S ribosomal subunit in complex with dirithromycin, fMet-Phe-tRNA(Phe) and deacylated tRNA(iMet).	ELECTRON MICROSCOPY	2.1	72
4	7RQ8\|1\|2x	Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.50A resolution	X-RAY DIFFRACTION	2.5	71
5	7RQ8\|1\|1x	Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with iboxamycin, mRNA, deacylated A- and E-site tRNAs, and aminoacylated P-site tRNA at 2.50A resolution	X-RAY DIFFRACTION	2.5	71
6	4Y4P\|1\|1x	Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to mRNA and A-, P- and E-site tRNAs at 2.5A resolution	X-RAY DIFFRACTION	2.5	72
7	4W2F\|1\|AX	Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites	X-RAY DIFFRACTION	2.4	72
8	6XHV\|1\|2x	Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.40A resolution	X-RAY DIFFRACTION	2.4	71
9	6XHV\|1\|1x	Crystal structure of the A2058-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.40A resolution	X-RAY DIFFRACTION	2.4	71
10	6XHW\|1\|1x	Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution	X-RAY DIFFRACTION	2.5	71
11	8CVL\|1\|1x	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMTHSMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.30A resolution	X-RAY DIFFRACTION	2.3	72
12	8CVJ\|1\|1x	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution	X-RAY DIFFRACTION	2.4	72
13	8CVK\|1\|1x	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution	X-RAY DIFFRACTION	2.5	72
14	6XHW\|1\|2x	Crystal structure of the A2058-unmethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.50A resolution	X-RAY DIFFRACTION	2.5	71
15	8CVJ\|1\|2x	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMSEAC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.40A resolution	X-RAY DIFFRACTION	2.4	72
16	8CVK\|1\|2x	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.50A resolution	X-RAY DIFFRACTION	2.5	72
17	8CVL\|1\|2x	Crystal structure of the Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-NH-tRNAphe, peptidyl P-site fMTHSMRC-NH-tRNAmet, and deacylated E-site tRNAphe at 2.30A resolution	X-RAY DIFFRACTION	2.3	72
18	4Y4P\|1\|2x	Crystal structure of the Thermus thermophilus 70S ribosome with rRNA modifications and bound to mRNA and A-, P- and E-site tRNAs at 2.5A resolution	X-RAY DIFFRACTION	2.5	72
19	4W2F\|1\|CX	Crystal structure of the Thermus thermophilus 70S ribosome in complex with amicoumacin, mRNA and three deacylated tRNAs in the A, P and E sites	X-RAY DIFFRACTION	2.4	72
20	7ZHG\|1\|4	High-resolution cryo-EM structure of Pyrococcus abyssi 30S ribosomal subunit bound to mRNA and initiator tRNA anticodon stem-loop	ELECTRON MICROSCOPY	2.25	18
21	7TOP\|1\|APTN	Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20	ELECTRON MICROSCOPY	2.4	77
22	6YSI\|1\|8+6YSI\|1\|6	Acinetobacter baumannii ribosome-tigecycline complex - 50S subunit	ELECTRON MICROSCOPY	2.5	8

Equivalence class NR_2.5_35542.104 Obsolete

Release history

Parents

Children