ISDA

Deposition Date 2006-08-04

Release Date 2014-07-09

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4V4H

Keywords:

RIBOSOME

Title:

Crystal structure of the bacterial ribosome from Escherichia coli in complex with the antibiotic kasugamyin at 3.5A resolution.

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.46 Å

R-Value Free:

0.33

R-Value Work:

0.27

R-Value Observed:

0.27

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S RIBOSOMAL RNA
Chain IDs:A (auth: AA), AB (auth: CA)
Chain Length:1542
Number of Molecules:2
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Gene (Uniprot):rpsB
Chain IDs:T (auth: AB), TB (auth: CB)
Chain Length:241
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7V0 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Gene (Uniprot):rpsC
Chain IDs:B (auth: AC), BB (auth: CC)
Chain Length:233
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:C (auth: AD), CB (auth: CD)
Chain Length:206
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Gene (Uniprot):rpsE
Chain IDs:D (auth: AE), DB (auth: CE)
Chain Length:167
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Gene (Uniprot):rpsF
Chain IDs:E (auth: AF), EB (auth: CF)
Chain Length:135
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P02358 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:F (auth: AG), FB (auth: CG)
Chain Length:179
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Gene (Uniprot):rpsH
Chain IDs:G (auth: AH), GB (auth: CH)
Chain Length:130
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7W7 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:H (auth: AI), HB (auth: CI)
Chain Length:130
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7X3 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Gene (Uniprot):rpsJ
Chain IDs:I (auth: AJ), IB (auth: CJ)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7R5 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Gene (Uniprot):rpsK
Chain IDs:J (auth: AK), JB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7R9 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Gene (Uniprot):rpsL
Chain IDs:K (auth: AL), KB (auth: CL)
Chain Length:124
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7S3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Gene (Uniprot):rpsM
Chain IDs:L (auth: AM), LB (auth: CM)
Chain Length:118
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7S9 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14
Gene (Uniprot):rpsN
Chain IDs:M (auth: AN), MB (auth: CN)
Chain Length:101
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG59 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Chain IDs:N (auth: AO), NB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0ADZ4 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Gene (Uniprot):rpsP
Chain IDs:O (auth: AP), OB (auth: CP)
Chain Length:82
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7T3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Gene (Uniprot):rpsQ
Chain IDs:P (auth: AQ), PB (auth: CQ)
Chain Length:84
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG63 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Gene (Uniprot):rpsR
Chain IDs:Q (auth: AR), QB (auth: CR)
Chain Length:75
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7T7 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Gene (Uniprot):rpsS
Chain IDs:R (auth: AS), RB (auth: CS)
Chain Length:92
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7U3 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Gene (Uniprot):rpsT
Chain IDs:S (auth: AT), SB (auth: CT)
Chain Length:87
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7U7 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S21
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), UB (auth: CU)
Chain Length:71
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P68679 Pfam ID:PF01165

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L32
Gene (Uniprot):rpmF
Chain IDs:UA (auth: B0), UC (auth: D0)
Chain Length:57
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7N4 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L33
Gene (Uniprot):rpmG
Chain IDs:VA (auth: B1), VC (auth: D1)
Chain Length:55
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7N9 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L34
Gene (Uniprot):rpmH
Chain IDs:WA (auth: B2), WC (auth: D2)
Chain Length:46
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7P5 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L35
Gene (Uniprot):rpmI
Chain IDs:XA (auth: B3), XC (auth: D3)
Chain Length:65
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7Q1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L36
Gene (Uniprot):rpmJ
Chain IDs:YA (auth: B4), YC (auth: D4)
Chain Length:38
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:V (auth: BA), VB (auth: DA)
Chain Length:120
Number of Molecules:2
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:W (auth: BB), WB (auth: DB)
Chain Length:2904
Number of Molecules:2
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L2
Gene (Uniprot):rplB
Chain IDs:Y (auth: BC), YB (auth: DC)
Chain Length:273
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L3
Gene (Uniprot):rplC
Chain IDs:Z (auth: BD), ZB (auth: DD)
Chain Length:209
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60438 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L4
Gene (Uniprot):rplD
Chain IDs:AA (auth: BE), AC (auth: DE)
Chain Length:201
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L5
Gene (Uniprot):rplE
Chain IDs:BA (auth: BF), BC (auth: DF)
Chain Length:179
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L6
Chain IDs:CA (auth: BG), CC (auth: DG)
Chain Length:177
Number of Molecules:2
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L9
Gene (Uniprot):rplI
Chain IDs:DA (auth: BH), DC (auth: DH)
Chain Length:149
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L11
Gene (Uniprot):rplK
Chain IDs:ZA (auth: BI), ZC (auth: DI)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L13
Chain IDs:EA (auth: BJ), EC (auth: DJ)
Chain Length:142
Number of Molecules:2
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L14
Chain IDs:FA (auth: BK), FC (auth: DK)
Chain Length:123
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0ADY3 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L15
Gene (Uniprot):rplO
Chain IDs:GA (auth: BL), GC (auth: DL)
Chain Length:144
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P02413 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L16
Chain IDs:HA (auth: BM), HC (auth: DM)
Chain Length:136
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0ADY7 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L17
Chain IDs:IA (auth: BN), IC (auth: DN)
Chain Length:127
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG44 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L18
Gene (Uniprot):rplR
Chain IDs:JA (auth: BO), JC (auth: DO)
Chain Length:117
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0C018 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L19
Gene (Uniprot):rplS
Chain IDs:KA (auth: BP), KC (auth: DP)
Chain Length:115
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7K6 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L20
Gene (Uniprot):rplT
Chain IDs:LA (auth: BQ), LC (auth: DQ)
Chain Length:118
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7L3 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L21
Chain IDs:MA (auth: BR), MC (auth: DR)
Chain Length:103
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG48 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L22
Gene (Uniprot):rplV
Chain IDs:NA (auth: BS), NC (auth: DS)
Chain Length:110
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L23
Chain IDs:OA (auth: BT), OC (auth: DT)
Chain Length:100
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0ADZ0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L24
Gene (Uniprot):rplX
Chain IDs:PA (auth: BU), PC (auth: DU)
Chain Length:104
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L25
Gene (Uniprot):rplY
Chain IDs:X (auth: BV), XB (auth: DV)
Chain Length:94
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P68919 Pfam ID:PF01386

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L27
Gene (Uniprot):rpmA
Chain IDs:QA (auth: BW), QC (auth: DW)
Chain Length:85
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7L8 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L29
Gene (Uniprot):rpmC
Chain IDs:RA (auth: BX), RC (auth: DX)
Chain Length:63
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7M6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L30
Chain IDs:SA (auth: BY), SC (auth: DY)
Chain Length:59
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0AG51 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L31
Gene (Uniprot):rpmE
Chain IDs:TA (auth: BZ), TC (auth: DZ)
Chain Length:70
Number of Molecules:2
Biological Source:Escherichia coli

UniProt ID:P0A7M9 Pfam ID:PF01197

Ligand Molecules

KSG

Primary Citation

Structural analysis of kasugamycin inhibition of translation.

Schuwirth, B.S, Day, J.M, Hau, C.W, Janssen, G.R, Dahlberg, A.E, Cate, J.H.D, Vila-Sanjurjo, A.Show

Nat.Struct.Mol.Biol. 13 879 886 (2006)

PMID: 16998486 DOI: 10.1038/nsmb1150

Abstact

The prokaryotic ribosome is an important target of antibiotic action. We determined the X-ray structure of the aminoglycoside kasugamycin (Ksg) in complex with the Escherichia coli 70S ribosome at 3.5-A resolution. The structure reveals that the drug binds within the messenger RNA channel of the 30S subunit between the universally conserved G926 and A794 nucleotides in 16S ribosomal RNA, which are sites of Ksg resistance. To our surprise, Ksg resistance mutations do not inhibit binding of the drug to the ribosome. The present structural and biochemical results indicate that inhibition by Ksg and Ksg resistance are closely linked to the structure of the mRNA at the junction of the peptidyl-tRNA and exit-tRNA sites (P and E sites).

Legend

Protein

Chemical

Disease

Primary Citation of related structures