5O61 image
Deposition Date 2017-06-03
Release Date 2017-07-12
Last Version Date 2024-05-15
Entry Detail
PDB ID:
5O61
Keywords:
RIBOSOME
Title:
The complete structure of the Mycobacterium smegmatis 70S ribosome
Biological Source:
Source Organism(s):
Mycobacterium smegmatis str. MC2 155 (Taxon ID: 246196)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.31 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5O61 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein bL37
Gene (Uniprot):MSMEG_1916
Chain IDs:A (auth: 3)
Chain Length:24
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QTP4 Pfam ID:PF26427
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:B (auth: A)
Chain Length:61
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:C (auth: B)
Chain Length:57
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:IA (auth: BA)
Chain Length:1528
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Conserved domain protein
Gene (Uniprot):MSMEG_0945
Chain IDs:JA (auth: BB)
Chain Length:33
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QR10 Pfam ID:PF08213
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:KA (auth: BC)
Chain Length:275
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD7 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:LA (auth: BD)
Chain Length:201
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSL7 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:MA (auth: BE)
Chain Length:214
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG6 Pfam ID:PF00333, PF03719
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:NA (auth: BF)
Chain Length:96
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:OA (auth: BG)
Chain Length:156
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QS97 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:PA (auth: BH)
Chain Length:132
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG3 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:QA (auth: BI)
Chain Length:150
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSP9 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:RA (auth: BJ)
Chain Length:101
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD0 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:SA (auth: BK)
Chain Length:138
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSL6 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:TA (auth: BL)
Chain Length:124
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QS96 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:UA (auth: BM)
Chain Length:124
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSL5 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 typ
Gene (Uniprot):rpsZ
Chain IDs:VA (auth: BN)
Chain Length:61
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG2 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:WA (auth: BO)
Chain Length:89
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QVQ3 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:XA (auth: BP)
Chain Length:156
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QV37 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:YA (auth: BQ)
Chain Length:98
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSE0 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18 2
Gene (Uniprot):rpsR2
Chain IDs:ZA (auth: BR)
Chain Length:84
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R7F7 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:AB (auth: BS)
Chain Length:93
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD5 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:BB (auth: BT)
Chain Length:86
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R102 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:CB (auth: BV)
Chain Length:277
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QVB8 Pfam ID:PF00318
Polymer Type:polyribonucleotide
Molecule:P/P-site Phe-tRNA(Phe)
Chain IDs:DB (auth: BW)
Chain Length:76
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
Polymer Type:polyribonucleotide
Molecule:mRNA fragment
Chain IDs:EB (auth: BX)
Chain Length:6
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:D (auth: C)
Chain Length:278
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD4 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:E (auth: D)
Chain Length:217
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD1 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:F (auth: E)
Chain Length:215
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD2 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:G (auth: F)
Chain Length:187
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG1 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:H (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG4 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:I (auth: H)
Chain Length:151
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R7F6 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:J (auth: I)
Chain Length:175
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QS62 Pfam ID:PF00466
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:K (auth: J)
Chain Length:142
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QS45 Pfam ID:PF03946, PF00298
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:L (auth: K)
Chain Length:147
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSP8 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:M (auth: L)
Chain Length:122
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSF9 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:N (auth: M)
Chain Length:147
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG8 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:O (auth: N)
Chain Length:138
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD8 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:P (auth: O)
Chain Length:199
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSL9 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:Q (auth: P)
Chain Length:127
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG5 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:R (auth: Q)
Chain Length:113
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QV42 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:S (auth: R)
Chain Length:129
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QYU6 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:T (auth: S)
Chain Length:103
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R151 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:U (auth: T)
Chain Length:153
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD6 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:V (auth: U)
Chain Length:100
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD3 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:W (auth: V)
Chain Length:105
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG0 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:X (auth: W)
Chain Length:215
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R3D2 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:Y (auth: X)
Chain Length:88
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R150 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein L28P
Chain IDs:Z (auth: Y)
Chain Length:64
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QV03 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:AA (auth: Z)
Chain Length:77
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSD9 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:BA (auth: a)
Chain Length:61
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSG7 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:CA (auth: b)
Chain Length:57
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R3I9 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33 1
Gene (Uniprot):rpmG1
Chain IDs:DA (auth: c)
Chain Length:278
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QS39 Pfam ID:PF00471
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:EA (auth: d)
Chain Length:217
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R7K0 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Gene (Uniprot):rpmI
Chain IDs:FA (auth: e)
Chain Length:215
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QYU7 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:GA (auth: f)
Chain Length:187
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0QSL4 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:HA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Mycobacterium smegmatis str. MC2 155
UniProt ID:A0R215 Pfam ID:PF01197
Ligand Molecules
MG
PHE
ZN
Primary Citation
The Complete Structure of the Mycobacterium smegmatis 70S Ribosome.
Cell Rep 20 149 160 (2017)
PMID: 28683309 DOI: 10.1016/j.celrep.2017.06.029

Abstact

The ribosome carries out the synthesis of proteins in every living cell. It consequently represents a frontline target in anti-microbial therapy. Tuberculosis ranks among the leading causes of death worldwide, due in large part to the combination of difficult-to-treat latency and antibiotic resistance. Here, we present the 3.3-Å cryo-EM structure of the 70S ribosome of Mycobacterium smegmatis, a close relative to the human pathogen Mycobacterium tuberculosis. The structure reveals two additional ribosomal proteins and localizes them to the vicinity of drug-target sites in both the catalytic center and the decoding site of the ribosome. Furthermore, we visualized actinobacterium-specific rRNA and protein expansions that extensively remodel the ribosomal surface with implications for polysome organization. Our results provide a foundation for understanding the idiosyncrasies of mycobacterial translation and reveal atomic details of the structure that will facilitate the design of anti-tubercular therapeutics.

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Protein

Chemical

Disease

Primary Citation of related structures
5O5J
5O60
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