6YEF image
Deposition Date 2020-03-24
Release Date 2021-01-27
Last Version Date 2025-03-12
Entry Detail
PDB ID:
6YEF
Keywords:
RIBOSOME
Title:
70S initiation complex with assigned rRNA modifications from Staphylococcus aureus
Biological Source:
Source Organism:
synthetic construct (Taxon ID: 32630)
Staphylococcus aureus subsp. aureus NCTC 8325 (Taxon ID: 93061)
Escherichia coli DH5[alpha] (Taxon ID: 668369)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.20 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6YEF validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:QA (auth: 0)
Chain Length:62
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FZ60 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:RA (auth: 1)
Chain Length:69
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW14 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:SA (auth: 2)
Chain Length:59
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:P0A0G2 Pfam ID:PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31 type B
Gene (Uniprot):rpmE2
Chain IDs:TA (auth: 3)
Chain Length:84
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FWD8 Pfam ID:PF01197
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:UA (auth: 4)
Chain Length:58
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FZF1 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 2
Gene (Uniprot):rpmG2
Chain IDs:VA (auth: 5)
Chain Length:49
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FY22 Pfam ID:PF00471
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:WA (auth: 6)
Chain Length:45
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FUQ0 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:XA (auth: 7)
Chain Length:66
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FXQ0 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:YA (auth: 8)
Chain Length:37
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW29 Pfam ID:PF00444
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:V (auth: A)
Chain Length:2923
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:W (auth: B)
Chain Length:115
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:X (auth: D)
Chain Length:277
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:P60430 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:Y (auth: E)
Chain Length:220
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW06 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:Z (auth: F)
Chain Length:207
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW07 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:AA (auth: G)
Chain Length:156
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW18 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:BA (auth: H)
Chain Length:178
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW21 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:CA (auth: M)
Chain Length:145
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW38 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:DA (auth: N)
Chain Length:89
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW16 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:EA (auth: O)
Chain Length:146
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:P0A0F8 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:FA (auth: P)
Chain Length:144
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW13 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:GA (auth: Q)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW33 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:HA (auth: R)
Chain Length:80
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW22 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:IA (auth: S)
Chain Length:92
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FZ42 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:JA (auth: T)
Chain Length:118
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FXQ1 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:KA (auth: U)
Chain Length:102
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FXS8 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:LA (auth: V)
Chain Length:117
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW11 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:MA (auth: W)
Chain Length:91
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW08 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:NA (auth: X)
Chain Length:77
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW17 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:OA (auth: Y)
Chain Length:217
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2G0S0 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:PA (auth: Z)
Chain Length:94
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FXT0 Pfam ID:PF01016
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:A (auth: a)
Chain Length:2923
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: b)
Chain Length:115
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FZ25 Pfam ID:PF00318
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: c)
Chain Length:217
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW12 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: d)
Chain Length:277
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FXK6 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: e)
Chain Length:220
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW23 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: f)
Chain Length:207
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2G113 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: g)
Chain Length:156
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:P48940 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: h)
Chain Length:178
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW20 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: i)
Chain Length:132
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW39 Pfam ID:PF00380
Polymer Type:polypeptide(L)
Molecule:ribosomal protein uS10
Chain IDs:J (auth: j)
Chain Length:102
Number of Molecules:1
Biological Source:Staphylococcus aureus subsp. aureus NCTC 8325
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: k)
Chain Length:129
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW31 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: l)
Chain Length:137
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:P0A0H0 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: m)
Chain Length:145
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW30 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Gene (Uniprot):rpsN
Chain IDs:N (auth: n)
Chain Length:89
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FYU5 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: o)
Chain Length:146
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2G2Q1 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: p)
Chain Length:144
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FZ45 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: q)
Chain Length:122
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW15 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: r)
Chain Length:80
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2G111 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: s)
Chain Length:92
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FW10 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: t)
Chain Length:118
Number of Molecules:1
Biological Source:Staphylococcus aureus (strain NCTC 8325)
UniProt ID:Q2FXY6 Pfam ID:PF01649
Polymer Type:polyribonucleotide
Molecule:mRNA
Chain IDs:U (auth: v)
Chain Length:117
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:P-site tRNA
Chain IDs:ZA (auth: x)
Chain Length:77
Number of Molecules:1
Biological Source:Escherichia coli DH5[alpha]
Ligand Molecules
K
MG
Primary Citation
Cryo-EM structure of the ribosome functional complex of the human pathogen Staphylococcus aureus at 3.2 angstrom resolution.
Febs Lett. 594 3551 3567 (2020)
PMID: 32852796 DOI: 10.1002/1873-3468.13915

Abstact

Staphylococcus aureus is a bacterial pathogen and one of the leading causes of healthcare-acquired infections in the world. The growing antibiotic resistance of S. aureus obliges us to search for new drugs and treatments. As the majority of antibiotics target the ribosome, knowledge of its detailed structure is crucial for drug development. Here, we report the cryo-EM reconstruction at 3.2 Å resolution of the S. aureus ribosome with P-site tRNA, messenger RNA, and 10 RNA modification sites previously not assigned or visualized. The resulting model is the most precise and complete high-resolution structure to date of the S. aureus 70S ribosome with functional ligands.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6YEF