ISDA

Entry Detail

PDB ID:

8G2A

Keywords:

Title:

Crystal structure of the A2503-C2,C8-dimethylated Thermus thermophilus 70S ribosome in complex with mRNA, aminoacylated A-site Phe-tRNAphe, peptidyl P-site fMTHSMRC-tRNAmet, and deacylated E-site tRNAphe at 2.45A resolution

Biological Source:

Source Organism:

Escherichia coli, Escherichia phage T4, Thermus thermophilus HB8

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2023-02-03

Release Date:

2023-12-27

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.45 Å

R-Value Free:

0.24

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

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

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

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

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

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

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

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

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

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

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

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

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

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

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

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

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

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

UniProt ID:Q5SKU1 Pfam ID:PF01632

Protein Blast

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

UniProt ID:Q5SHR2 Pfam ID:PF00444

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

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

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L2
Chain IDs:C (auth: 1D), HB (auth: 2D)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

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

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

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

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L5
Chain IDs:F (auth: 1G), KB (auth: 2G)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L6
Chain IDs:G (auth: 1H), LB (auth: 2H)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY8 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L9
Chain IDs:H (auth: 1I), MB (auth: 2I)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Protein Blast

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

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L14
Chain IDs:J (auth: 1O), OB (auth: 2O)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L15
Chain IDs:K (auth: 1P), PB (auth: 2P)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

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

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L17
Chain IDs:M (auth: 1R), RB (auth: 2R)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L18
Chain IDs:N (auth: 1S), SB (auth: 2S)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

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

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L20
Chain IDs:P (auth: 1U), UB (auth: 2U)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L21
Chain IDs:Q (auth: 1V), VB (auth: 2V)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L22
Chain IDs:R (auth: 1W), WB (auth: 2W)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

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

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L24
Chain IDs:T (auth: 1Y), YB (auth: 2Y)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Description:50S ribosomal protein L25
Chain IDs:U (auth: 1Z), ZB (auth: 2Z)
Chain Length:7
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

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

Protein Blast

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

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

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

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S4
Chain IDs:IA (auth: 1d), NC (auth: 2d)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

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

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

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

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S7
Chain IDs:LA (auth: 1g), QC (auth: 2g)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S8
Chain IDs:MA (auth: 1h), RC (auth: 2h)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P0DOY9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S9
Chain IDs:NA (auth: 1i), SC (auth: 2i)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

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

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

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

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

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

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

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

UniProt ID:P80377 Pfam ID:PF00416

Protein Blast

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

UniProt ID:P0DOY6 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S15
Chain IDs:TA (auth: 1o), YC (auth: 2o)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S16
Chain IDs:UA (auth: 1p), ZC (auth: 2p)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SJH3 Pfam ID:PF00886

Protein Blast

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

UniProt ID:P0DOY7 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S18
Chain IDs:WA (auth: 1r), BD (auth: 2r)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein S19
Chain IDs:XA (auth: 1s), CD (auth: 2s)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

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

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Description:30S ribosomal protein Thx
Chain IDs:ZA (auth: 1u), ED (auth: 2u)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus HB8

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Description:MF-mRNA
Chain IDs:AB (auth: 1v), FD (auth: 2v)
Chain Length:101
Number of Molecules:2
Biological Source:Escherichia phage T4

Polymer Type:polyribonucleotide
Description:A-site Aminoacylated Phe-tRNAphe
Chain IDs:BB (auth: 1w), GD (auth: 2w)
Chain Length:76
Number of Molecules:2
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Description:P-site Peptidyl-tRNA fMTHSMRC-tRNAmet RNA-part
Chain IDs:CB (auth: 1x), HD (auth: 2x)
Chain Length:96
Number of Molecules:2
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Description:E-site Deacylated tRNAphe
Chain IDs:EB (auth: 1y), JD (auth: 2y)
Chain Length:110
Number of Molecules:2
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Description:P-site Peptidyl-tRNA fMTHSMRC-tRNAmet Peptide-part
Chain IDs:DB (auth: 1z), ID (auth: 2z)
Chain Length:7
Number of Molecules:2
Biological Source:Escherichia coli

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
0TD	QA	ASP	modified residue
2MG	FA	G	modified residue
4OC	FA	C	modified residue
4SU	BB	U	modified residue
5MC	FA	C	modified residue
5MU	BB	U	modified residue
8AN	CB	A	modified residue
F3N	BB	A	modified residue
G7M	FA	G	modified residue
M2G	FA	G	modified residue
MA6	FA	A	modified residue
MIA	BB	A	modified residue
PSU	FA	U	modified residue
UR3	FA	U	modified residue

Ligand Molecules

SF4

Primary Citation

Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it.

Aleksandrova, E.V, Wu, K.J.Y, Tresco, B.I.C, Syroegin, E.A, Killeavy, E.E, Balasanyants, S.M, Svetlov, M.S, Gregory, S.T, Atkinson, G.C, Myers, A.G, Polikanov, Y.S.Show

Nat.Chem.Biol. 20 867 876 (2024)

PMID: 38238495 DOI: 10.1038/s41589-023-01525-w

Abstact

The bacterial ribosome is an essential drug target as many clinically important antibiotics bind and inhibit its functional centers. The catalytic peptidyl transferase center (PTC) is targeted by the broadest array of inhibitors belonging to several chemical classes. One of the most abundant and clinically prevalent resistance mechanisms to PTC-acting drugs in Gram-positive bacteria is C8-methylation of the universally conserved A2503 nucleobase by Cfr methylase in 23S ribosomal RNA. Despite its clinical importance, a sufficient understanding of the molecular mechanisms underlying Cfr-mediated resistance is currently lacking. Here, we report a set of high-resolution structures of the Cfr-modified 70S ribosome containing aminoacyl- and peptidyl-transfer RNAs. These structures reveal an allosteric rearrangement of nucleotide A2062 upon Cfr-mediated methylation of A2503 that likely contributes to the reduced potency of some PTC inhibitors. Additionally, we provide the structural bases behind two distinct mechanisms of engaging the Cfr-methylated ribosome by the antibiotics iboxamycin and tylosin.

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Protein

Chemical

Disease

Primary Citation of related structures