ISDA: 6S13

Deposition Date 2019-06-18

Release Date 2019-08-21

Last Version Date 2024-11-13

Entry Detail

PDB ID:

6S13

Keywords:

RIBOSOME

Title:

Erythromycin Resistant Staphylococcus aureus 70S ribosome (delta R88 A89 uL22).

Biological Source:

Source Organism:

Staphylococcus aureus (Taxon ID: 1280)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

3.58 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG2
Chain IDs:AA (auth: 1)
Chain Length:47
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077V2P0 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BA (auth: 2)
Chain Length:43
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TQ59 Pfam ID:PF00468

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:CA (auth: 3)
Chain Length:64
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UL47 Pfam ID:PF01632

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:DA (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UGV8 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A
Chain Length:1539
Number of Molecules:1
Biological Source:Staphylococcus aureus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B
Chain Length:226
Number of Molecules:1
Biological Source:Staphylococcus aureus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rap
Chain IDs:C
Chain Length:202
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:B3VKN3 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
Chain Length:198
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8U3W0 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
Chain Length:206
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TRC7 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
Chain Length:175
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TUC3 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
Chain Length:175
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8U3X2 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:H
Chain Length:131
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TUE6 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UUA0 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:J
Chain Length:146
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UGA7 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:K
Chain Length:114
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077V4G0 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:L
Chain Length:135
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UG91 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:M
Chain Length:119
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TRE0 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:N
Chain Length:60
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UVB6 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:O
Chain Length:116
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077VMP6 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:P
Chain Length:102
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:D7URR3 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:Q
Chain Length:110
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UKF9 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:R
Chain Length:54
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TUB4 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:S
Chain Length:80
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TRD5 Pfam ID:PF00467, PF17136

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:T
Chain Length:94
Number of Molecules:1
Biological Source:Staphylococcus aureus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:U
Chain Length:52
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077ULC5 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:V
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077URJ8 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:W
Chain Length:67
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077W1J5 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:X
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8UVN7 Pfam ID:PF00327

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31 type B
Gene (Uniprot):rpmE2
Chain IDs:Y
Chain Length:59
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A380EL30 Pfam ID:PF01197

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:Z
Chain Length:48
Number of Molecules:1
Biological Source:Staphylococcus aureus

Polymer Type:polyribonucleotide
Molecule:16S ribosomal RNA
Chain IDs:EA (auth: a)
Chain Length:1539
Number of Molecules:1
Biological Source:Staphylococcus aureus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:FA (auth: b)
Chain Length:226
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A2X2M020 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:GA (auth: c)
Chain Length:202
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UU26 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:HA (auth: d)
Chain Length:198
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TVK2 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:IA (auth: e)
Chain Length:206
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TUC9 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:JA (auth: f)
Chain Length:175
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8TPC6 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:KA (auth: g)
Chain Length:175
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077VHU6 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:LA (auth: h)
Chain Length:131
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8U8T8 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:MA (auth: i)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A1Q4GY48 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:NA (auth: j)
Chain Length:146
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A0H2K0A0 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:OA (auth: k)
Chain Length:114
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UKD6 Pfam ID:PF00411

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:PA (auth: l)
Chain Length:135
Number of Molecules:1
Biological Source:Staphylococcus aureus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:QA (auth: m)
Chain Length:119
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8U8U6 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsN_1
Chain IDs:RA (auth: n)
Chain Length:60
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UGW7 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:SA (auth: o)
Chain Length:116
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8U6H8 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:TA (auth: p)
Chain Length:102
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8U6K4 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:UA (auth: q)
Chain Length:110
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077VLD5 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:VA (auth: r)
Chain Length:54
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:A0A077UZF4 Pfam ID:PF01084

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:WA (auth: s)
Chain Length:80
Number of Molecules:1
Biological Source:Staphylococcus aureus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:XA (auth: t)
Chain Length:94
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:W8UXC3 Pfam ID:PF01649

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S21
Chain IDs:YA (auth: u)
Chain Length:52
Number of Molecules:1
Biological Source:Staphylococcus aureus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Ribosome hibernation promoting factor
Chain IDs:ZA (auth: v)
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus

UniProt ID:D2Z097 Pfam ID:PF02482, PF16321

Ligand Molecules

Primary Citation

Exit tunnel modulation as resistance mechanism of S. aureus erythromycin resistant mutant.

Halfon, Y, Matzov, D, Eyal, Z, Bashan, A, Zimmerman, E, Kjeldgaard, J, Ingmer, H, Yonath, A.Show

Sci Rep 9 11460 11460 (2019)

PMID: 31391518 DOI: 10.1038/s41598-019-48019-1

Abstact

The clinical use of the antibiotic erythromycin (ery) is hampered owing to the spread of resistance genes that are mostly mutating rRNA around the ery binding site at the entrance to the protein exit tunnel. Additional effective resistance mechanisms include deletion or insertion mutations in ribosomal protein uL22, which lead to alterations of the exit tunnel shape, located 16 Å away from the drug's binding site. We determined the cryo-EM structures of the Staphylococcus aureus 70S ribosome, and its ery bound complex with a two amino acid deletion mutation in its ß hairpin loop, which grants the bacteria resistance to ery. The structures reveal that, although the binding of ery is stable, the movement of the flexible shorter uL22 loop towards the tunnel wall creates a wider path for nascent proteins, thus enabling bypass of the barrier formed by the drug. Moreover, upon drug binding, the tunnel widens further.

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Protein

Chemical

Disease

Primary Citation of related structures