ISDA: 4WT8

Deposition Date 2014-10-29

Release Date 2015-01-21

Last Version Date 2024-11-20

Entry Detail

PDB ID:

4WT8

Keywords:

RIBOSOME

Title:

Crystal Structure of bactobolin A bound to 70S ribosome-tRNA complex

Biological Source:

Source Organism:

Thermus thermophilus (Taxon ID: 300852)
Thermus thermophilus (Taxon ID: 308052)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.40 Å

R-Value Free:

0.24

R-Value Work:

0.20

R-Value Observed:

0.20

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:A (auth: A2)
Chain Length:9
Number of Molecules:1
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AA), Y (auth: BA)
Chain Length:234
Number of Molecules:2
Biological Source:Thermus thermophilus

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:C (auth: AC)
Chain Length:238
Number of Molecules:1
Biological Source:Thermus thermophilus

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:D (auth: AD), AA (auth: BD)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus

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:E (auth: AE), BA (auth: BE)
Chain Length:150
Number of Molecules:2
Biological Source:Thermus thermophilus

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:F (auth: AF), CA (auth: BF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

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:G (auth: AG), DA (auth: BG)
Chain Length:155
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P17291 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:H (auth: AH), EA (auth: BH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

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:I (auth: AI), FA (auth: BI)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus

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:J (auth: AJ), GA (auth: BJ)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

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:K (auth: AK), HA (auth: BK)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus

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:L (auth: AL), IA (auth: BL)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus

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:M (auth: AM), JA (auth: BM)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P80377 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:N (auth: AN), KA (auth: BN)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

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:O (auth: AO), LA (auth: BO)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

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:P (auth: AP), MA (auth: BP)
Chain Length:83
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SJH3 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:Q (auth: AR), NA (auth: BR)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

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:R (auth: AS), OA (auth: BS)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus

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:S (auth: AT), PA (auth: BT)
Chain Length:78
Number of Molecules:2
Biological Source:Thermus thermophilus

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:T (auth: AU), QA (auth: BU)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

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:U (auth: AW), RA (auth: BW)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:RNA (1504-MER)
Chain IDs:V (auth: Ab), X (auth: Bb)
Chain Length:1504
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:W (auth: B2)
Chain Length:10
Number of Molecules:1
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:Z (auth: BC)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:ZB (auth: C0), JD (auth: D0)
Chain Length:36
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHR2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S rRNA (2899-MER)
Chain IDs:AC (auth: C1), LD (auth: D1)
Chain Length:2899
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:A site tNA, E site tNA
Chain IDs:SA (auth: C2), TA (auth: C3), DC (auth: D3)
Chain Length:76
Number of Molecules:3
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:P site trNA
Chain IDs:UA (auth: C4)
Chain Length:77
Number of Molecules:1
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:UB (auth: C5), ED (auth: D5)
Chain Length:30
Number of Molecules:2
Biological Source:Thermus thermophilus

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:VB (auth: C6), FD (auth: D6)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus

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:WB (auth: C7), GD (auth: D7)
Chain Length:44
Number of Molecules:2
Biological Source:Thermus thermophilus

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:XB (auth: C8), HD (auth: D8)
Chain Length:48
Number of Molecules:2
Biological Source:Thermus thermophilus

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:YB (auth: C9), ID (auth: D9)
Chain Length:63
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SKU1 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:VA (auth: CA)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP7 Pfam ID:PF00687

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:WA (auth: CB), GC (auth: DB)
Chain Length:271
Number of Molecules:2
Biological Source:Thermus thermophilus

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:XA (auth: CC), HC (auth: DC)
Chain Length:204
Number of Molecules:2
Biological Source:Thermus thermophilus

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:YA (auth: CD), IC (auth: DD)
Chain Length:207
Number of Molecules:2
Biological Source:Thermus thermophilus

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:ZA (auth: CE), JC (auth: DE)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:AB (auth: CF), KC (auth: DF)
Chain Length:159
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P0DOY8 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:RB (auth: CH), BD (auth: DH)
Chain Length:93
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60494 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:BB (auth: CI), LC (auth: DI)
Chain Length:145
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Polymer Type:polypeptide(L)
Molecule:ribosomal L10 protein
Chain IDs:CB (auth: CJ), MC (auth: DJ)
Chain Length:130
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:SB (auth: CK), CD (auth: DK)
Chain Length:71
Number of Molecules:2
Biological Source:Thermus thermophilus

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:TB (auth: CL), DD (auth: DL)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:DB (auth: CM), NC (auth: DM)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

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:EB (auth: CN), OC (auth: DN)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

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:FB (auth: CO), PC (auth: DO)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

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:GB (auth: CP), QC (auth: DP)
Chain Length:141
Number of Molecules:2
Biological Source:Thermus thermophilus

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:HB (auth: CQ), RC (auth: DQ)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

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:IB (auth: CR), SC (auth: DR)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

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:JB (auth: CS), TC (auth: DS)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

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:KB (auth: CT), UC (auth: DT)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

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:LB (auth: CU), VC (auth: DU)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

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:MB (auth: CW)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus

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:NB (auth: CX), XC (auth: DX)
Chain Length:92
Number of Molecules:2
Biological Source:Thermus thermophilus

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:OB (auth: CY), YC (auth: DY)
Chain Length:100
Number of Molecules:2
Biological Source:Thermus thermophilus

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:PB (auth: CZ), ZC (auth: DZ)
Chain Length:176
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:QB (auth: Ca), AD (auth: Da)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P60493 Pfam ID:PF01016

Polymer Type:polyribonucleotide
Molecule:5S rRNA (119-MER)
Chain IDs:BC (auth: Cs), KD (auth: Ds)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:tRNA (5'-D(*AP*UP*CP*CP*CP*CP*GP*UP*GP*UP*CP*CP*UP*UP*GP*GP*UP*UP*CP*G)-3')
Chain IDs:CC (auth: D2)
Chain Length:20
Number of Molecules:1
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:tRNA (76-MER)
Chain IDs:EC (auth: D4)
Chain Length:76
Number of Molecules:1
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Gene (Uniprot):rplA
Chain IDs:FC (auth: DA)
Chain Length:84
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SLP7 Pfam ID:PF00687

Polymer Type:polyribonucleotide
Molecule:DNA (55-MER)
Chain IDs:MD (auth: DV)
Chain Length:55
Number of Molecules:1
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:WC (auth: DW)
Chain Length:113
Number of Molecules:1
Biological Source:Thermus thermophilus

UniProt ID:Q5SHP3 Pfam ID:PF00237

Ligand Molecules

3V6

PAR

Primary Citation

Bactobolin A Binds to a Site on the 70S Ribosome Distinct from Previously Seen Antibiotics.

Amunts, A, Fiedorczuk, K, Truong, T.T, Chandler, J, Peter Greenberg, E, Ramakrishnan, V.Show

J.Mol.Biol. 427 753 755 (2015)

PMID: 25562208 DOI: 10.1016/j.jmb.2014.12.018

Abstact

The ribosome is the target of a large number of antibiotics. Here, we report a 3.4-Å-resolution crystal structure of bactobolin A bound to 70S ribosome-tRNA complex. The antibiotic binds at a previously unseen site in the 50S subunit and displaces tRNA bound at the P-site. It thus likely has a similar mechanism of action as blasticidin S despite binding to a different site. The structure also rationalizes previously identified resistance mutations.

Legend

Protein

Chemical

Disease

Primary Citation of related structures