ISDA: 8EV7

Deposition Date 2022-10-19

Release Date 2023-08-09

Last Version Date 2025-03-19

Entry Detail

PDB ID:

8EV7

Keywords:

RIBOSOME

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with kanamycin, mRNA, and A-, P-, and E-site tRNAs

Biological Source:

Source Organism(s):

Escherichia coli (Taxon ID: 562)
Escherichia phage T4 (Taxon ID: 10665)
Thermus thermophilus HB8 (Taxon ID: 300852)

Expression System(s):

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.89 Å

R-Value Free:

0.26

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: 10), ZB (auth: 20)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60493 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:W (auth: 11), AC (auth: 21)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60494 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:X (auth: 12), BC (auth: 22)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP6 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:Y (auth: 13), CC (auth: 23)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:Z (auth: 14), DC (auth: 24)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SJE1 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:AA (auth: 15), EC (auth: 25)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80339 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:BA (auth: 16), FC (auth: 26)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P35871 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:CA (auth: 17), GC (auth: 27)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80340 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:DA (auth: 18), HC (auth: 28)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SKU1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:EA (auth: 19), IC (auth: 29)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHR2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:A (auth: 1A), EB (auth: 2A)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:B (auth: 1B), FB (auth: 2B)
Chain Length:121
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: 1D), GB (auth: 2D)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: 1E), HB (auth: 2E)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHN8 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: 1F), IB (auth: 2F)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHN9 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: 1G), JB (auth: 2G)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:G (auth: 1H), KB (auth: 2H)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY8 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: 1I), LB (auth: 2I)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:I (auth: 1N), MB (auth: 2N)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60488 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:J (auth: 1O), NB (auth: 2O)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP8 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:K (auth: 1P), OB (auth: 2P)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:L (auth: 1Q), PB (auth: 2Q)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60489 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:M (auth: 1R), QB (auth: 2R)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:N (auth: 1S), RB (auth: 2S)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:O (auth: 1T), SB (auth: 2T)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60490 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:P (auth: 1U), TB (auth: 2U)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60491 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:Q (auth: 1V), UB (auth: 2V)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60492 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: 1W), VB (auth: 2W)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP3 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:S (auth: 1X), WB (auth: 2X)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP0 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: 1Y), XB (auth: 2Y)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: 1Z), YB (auth: 2Z)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:FA (auth: 1a), JC (auth: 2a)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:GA (auth: 1b), KC (auth: 2b)
Chain Length:121
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80371 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:HA (auth: 1c), LC (auth: 2c)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:IA (auth: 1d), MC (auth: 2d)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:JA (auth: 1e), NC (auth: 2e)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:KA (auth: 1f), OC (auth: 2f)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SLP8 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:LA (auth: 1g), PC (auth: 2g)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P17291 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:MA (auth: 1h), QC (auth: 2h)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY9 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:NA (auth: 1i), RC (auth: 2i)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80374 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:OA (auth: 1j), SC (auth: 2j)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHN7 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:PA (auth: 1k), TC (auth: 2k)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80376 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:QA (auth: 1l), UC (auth: 2l)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHN3 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:RA (auth: 1m), VC (auth: 2m)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80377 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:SA (auth: 1n), WC (auth: 2n)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY6 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:TA (auth: 1o), XC (auth: 2o)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SJ76 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:UA (auth: 1p), YC (auth: 2p)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SJH3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:VA (auth: 1q), ZC (auth: 2q)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY7 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:WA (auth: 1r), AD (auth: 2r)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:XA (auth: 1s), BD (auth: 2s)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP2 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:YA (auth: 1t), CD (auth: 2t)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80380 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:ZA (auth: 1u), DD (auth: 2u)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:AB (auth: 1v), ED (auth: 2v)
Chain Length:24
Number of Molecules:2
Biological Source:Escherichia phage T4

Polymer Type:polyribonucleotide
Molecule:A-site and E-site tRNAs
Chain IDs:BB (auth: 1w), DB (auth: 1y), FD (auth: 2w), HD (auth: 2y)
Chain Length:113
Number of Molecules:4
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:CB (auth: 1x), GD (auth: 2x)
Chain Length:96
Number of Molecules:2
Biological Source:Escherichia coli

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
0TD	QA	ASP	modified residue
2MA	A	A	modified residue
2MG	FA	G	modified residue
2MU	A	U	modified residue
4OC	A	C	modified residue
4SU	BB	U	modified residue
5MC	A	C	modified residue
5MU	A	U	modified residue
7MG	FA	G	modified residue
M2G	FA	G	modified residue
MA6	FA	A	modified residue
MIA	BB	A	modified residue
OMG	A	G	modified residue
PSU	A	U	modified residue
UR3	FA	U	modified residue

Ligand Molecules

KAN

SF4

Primary Citation

Molecular basis of the pleiotropic effects by the antibiotic amikacin on the ribosome.

Seely, S.M, Parajuli, N.P, De Tarafder, A, Ge, X, Sanyal, S, Gagnon, M.G.Show

Nat Commun 14 4666 4666 (2023)

PMID: 37537169 DOI: 10.1038/s41467-023-40416-5

Abstact

Aminoglycosides are a class of antibiotics that bind to ribosomal RNA and exert pleiotropic effects on ribosome function. Amikacin, the semisynthetic derivative of kanamycin, is commonly used for treating severe infections with multidrug-resistant, aerobic Gram-negative bacteria. Amikacin carries the 4-amino-2-hydroxy butyrate (AHB) moiety at the N1 amino group of the central 2-deoxystreptamine (2-DOS) ring, which may confer amikacin a unique ribosome inhibition profile. Here we use in vitro fast kinetics combined with X-ray crystallography and cryo-EM to dissect the mechanisms of ribosome inhibition by amikacin and the parent compound, kanamycin. Amikacin interferes with tRNA translocation, release factor-mediated peptidyl-tRNA hydrolysis, and ribosome recycling, traits attributed to the additional interactions amikacin makes with the decoding center. The binding site in the large ribosomal subunit proximal to the 3'-end of tRNA in the peptidyl (P) site lays the groundwork for rational design of amikacin derivatives with improved antibacterial properties.

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Protein

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Disease

Primary Citation of related structures

Abstact

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