ISDA

Deposition Date 2014-09-12

Release Date 2014-10-15

Last Version Date 2023-12-27

Entry Detail

PDB ID:

4W2I

Keywords:

RIBOSOME/ANTIBIOTIC

Title:

Crystal structure of the Thermus thermophilus 70S ribosome in complex with negamycin, mRNA and three deacylated tRNAs in the A, P and E sites

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)
synthetic construct (Taxon ID: 32630)
Thermus thermophilus (Taxon ID: 300852)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.70 Å

R-Value Free:

0.25

R-Value Work:

0.20

R-Value Observed:

0.21

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S Ribosomal RNA
Chain IDs:A (auth: AA), EB (auth: CA)
Chain Length:1521
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), FB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), GB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD), HB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE), IB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF), JB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), KB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S8
Chain IDs:H (auth: AH), LB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), MB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), NB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), OB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), PB (auth: CL)
Chain Length:132
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), QB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80377 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S14
Chain IDs:N (auth: AN), RB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), SB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), TB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SJH3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S17
Chain IDs:Q (auth: AQ), UB (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), VB (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), WB (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), XB (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S Ribosomal Protein THX
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), YB (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:V (auth: AV), ZB (auth: CV)
Chain Length:24
Number of Molecules:2
Biological Source:synthetic construct

Polymer Type:polyribonucleotide
Molecule:A/P-site tRNA
Chain IDs:W (auth: AW), Y (auth: AY), AC (auth: CW), CC (auth: CY)
Chain Length:76
Number of Molecules:4
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:E-site tRNA
Chain IDs:X (auth: AX), BC (auth: CX)
Chain Length:77
Number of Molecules:2
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L27
Gene (Uniprot):rpmA
Chain IDs:UA (auth: B0), YC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L28
Gene (Uniprot):rpmB
Chain IDs:VA (auth: B1), ZC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L29
Gene (Uniprot):rpmC
Chain IDs:WA (auth: B2), AD (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L30
Gene (Uniprot):rpmD
Chain IDs:XA (auth: B3), BD (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L31
Gene (Uniprot):rpmE
Chain IDs:YA (auth: B4), CD (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L32
Gene (Uniprot):rpmF
Chain IDs:ZA (auth: B5), DD (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L33
Gene (Uniprot):rpmG
Chain IDs:AB (auth: B6), ED (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L34
Gene (Uniprot):rpmH
Chain IDs:BB (auth: B7), FD (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L35
Gene (Uniprot):rpmI
Chain IDs:CB (auth: B8), GD (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SKU1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L36
Gene (Uniprot):rpmJ
Chain IDs:DB (auth: B9), HD (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHR2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S Ribosomal RNA
Chain IDs:Z (auth: BA), DC (auth: DA)
Chain Length:2915
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:AA (auth: BB), EC (auth: DB)
Chain Length:121
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L2
Gene (Uniprot):rplB
Chain IDs:BA (auth: BD), FC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L3
Gene (Uniprot):rplC
Chain IDs:CA (auth: BE), GC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L4
Gene (Uniprot):rplD
Chain IDs:DA (auth: BF), HC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L5
Gene (Uniprot):rplE
Chain IDs:EA (auth: BG), IC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L6
Chain IDs:FA (auth: BH), JC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:Thermus thermophilus

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L9
Gene (Uniprot):rplI
Chain IDs:GA (auth: BI), KC (auth: DI)
Chain Length:148
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L13
Gene (Uniprot):rplM
Chain IDs:HA (auth: BN), LC (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L14
Gene (Uniprot):rplN
Chain IDs:IA (auth: BO), MC (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L15
Gene (Uniprot):rplO
Chain IDs:JA (auth: BP), NC (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L16
Gene (Uniprot):rplP
Chain IDs:KA (auth: BQ), OC (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L17
Gene (Uniprot):rplQ
Chain IDs:LA (auth: BR), PC (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L18
Gene (Uniprot):rplR
Chain IDs:MA (auth: BS), QC (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L19
Gene (Uniprot):rplS
Chain IDs:NA (auth: BT), RC (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L20
Gene (Uniprot):rplT
Chain IDs:OA (auth: BU), SC (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L21
Gene (Uniprot):rplU
Chain IDs:PA (auth: BV), TC (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L22
Gene (Uniprot):rplV
Chain IDs:QA (auth: BW), UC (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L23
Gene (Uniprot):rplW
Chain IDs:RA (auth: BX), VC (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L24
Gene (Uniprot):rplX
Chain IDs:SA (auth: BY), WC (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S Ribosomal Protein L25
Gene (Uniprot):rplY
Chain IDs:TA (auth: BZ), XC (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
4SU	W	U	4-THIOURIDINE-5'-MONOPHOSPHATE
5MC	X	C	5-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MU	W	U	5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG	W	G	?
MIA	W	A	?
PSU	W	U	PSEUDOURIDINE-5'-MONOPHOSPHATE

Ligand Molecules

NEG

SF4

Primary Citation

Negamycin Interferes with Decoding and Translocation by Simultaneous Interaction with rRNA and tRNA.

Polikanov, Y.S, Szal, T, Jiang, F, Gupta, P, Matsuda, R, Shiozuka, M, Steitz, T.A, Vazquez-Laslop, N, Mankin, A.S.Show

Mol.Cell 56 541 550 (2014)

PMID: 25306922 DOI: 10.1016/j.molcel.2014.09.021

Abstact

Negamycin (NEG) is a ribosome-targeting antibiotic that exhibits clinically promising activity. Its binding site and mode of action have remained unknown. We solved the structure of the Thermus thermophilus ribosome bound to mRNA and three tRNAs, in complex with NEG. The drug binds to both small and large ribosomal subunits at nine independent sites. Resistance mutations in the 16S rRNA unequivocally identified the binding site in the vicinity of the conserved helix 34 (h34) in the small subunit as the primary site of antibiotic action in the bacterial and, possibly, eukaryotic ribosome. At this site, NEG contacts 16S rRNA as well as the anticodon loop of the A-site tRNA. Although the NEG site of action overlaps with that of tetracycline (TET), the two antibiotics exhibit different activities: while TET sterically hinders binding of aminoacyl-tRNA to the ribosome, NEG stabilizes its binding, thereby inhibiting translocation and stimulating miscoding.

Legend

Protein

Chemical

Disease

Primary Citation of related structures