5V93 image
Deposition Date 2017-03-22
Release Date 2017-09-20
Last Version Date 2020-08-12
Entry Detail
PDB ID:
5V93
Keywords:
RIBOSOME
Title:
Cryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin
Biological Source:
Source Organism:
Mycobacterium tuberculosis (Taxon ID: 1773)
Streptomyces puniceus (Taxon ID: 67351)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.00 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5V93 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:A (auth: 0)
Chain Length:57
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH99 Pfam ID:PF01783
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:B (auth: 1)
Chain Length:55
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:C (auth: 2)
Chain Length:47
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH93 Pfam ID:PF00468
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:D (auth: 3)
Chain Length:64
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH91 Pfam ID:PF01632
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:E (auth: 4)
Chain Length:37
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH89 Pfam ID:PF00444
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:F (auth: 6)
Chain Length:80
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHA1 Pfam ID:PF01197
Polymer Type:polyribonucleotide
Molecule:23S rRNA
Chain IDs:G (auth: A)
Chain Length:3138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Polymer Type:polyribonucleotide
Molecule:5S rRNA
Chain IDs:H (auth: B)
Chain Length:115
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:I (auth: C)
Chain Length:274
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH99 Pfam ID:PF01783
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:J (auth: D)
Chain Length:201
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH87 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:K (auth: E)
Chain Length:223
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH85 Pfam ID:PF00573
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:L (auth: F)
Chain Length:96
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH83 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:M (auth: G)
Chain Length:179
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH81 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:N (auth: H)
Chain Length:152
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH79 Pfam ID:PF01281, PF03948
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:O (auth: J)
Chain Length:147
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHE1 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:P (auth: K)
Chain Length:139
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHD9 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:Q (auth: L)
Chain Length:124
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHD7 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:R (auth: M)
Chain Length:138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHD5 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:S (auth: N)
Chain Length:180
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHD3 Pfam ID:PF01196
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:T (auth: O)
Chain Length:122
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHD1 Pfam ID:PF00861
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:U (auth: P)
Chain Length:113
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHC9 Pfam ID:PF01245
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:V (auth: Q)
Chain Length:129
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHC5 Pfam ID:PF00453
Protein Blast
Polymer Type:polypeptide(L)
Molecule:LSU ribosomal protein L21p
Chain IDs:W (auth: R)
Chain Length:84
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHC3 Pfam ID:PF00829
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:X (auth: S)
Chain Length:93
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHC1 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:Y (auth: T)
Chain Length:100
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHB9 Pfam ID:PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:Z (auth: U)
Chain Length:105
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHB7 Pfam ID:PF00467, PF17136
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:AA (auth: V)
Chain Length:215
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHB5 Pfam ID:PF01386, PF14693
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:BA (auth: W)
Chain Length:86
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHB3 Pfam ID:PF01016
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:CA (auth: X)
Chain Length:33
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P0DV54 Pfam ID:PF00830
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:DA (auth: Y)
Chain Length:77
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHA7 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:EA (auth: Z)
Chain Length:65
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WHA3 Pfam ID:PF00327
Polymer Type:polyribonucleotide
Molecule:16S rRNA
Chain IDs:FA (auth: a)
Chain Length:3138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
Polymer Type:polypeptide(L)
Molecule:Capreomycin
Chain IDs:GA (auth: b)
Chain Length:115
Number of Molecules:1
Biological Source:Streptomyces puniceus
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:HA (auth: c)
Chain Length:274
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH37 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:IA (auth: d)
Chain Length:201
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH35 Pfam ID:PF00163, PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:JA (auth: e)
Chain Length:223
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH33 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:KA (auth: f)
Chain Length:96
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH31 Pfam ID:PF01250
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:LA (auth: g)
Chain Length:179
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH29 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:MA (auth: h)
Chain Length:152
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH27 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:NA (auth: i)
Chain Length:151
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH25 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:OA (auth: j)
Chain Length:147
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH67 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:PA (auth: k)
Chain Length:139
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH65 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:QA (auth: l)
Chain Length:124
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH63 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:RA (auth: m)
Chain Length:138
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH61 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Chain IDs:SA (auth: n)
Chain Length:180
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH57 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:TA (auth: o)
Chain Length:122
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH55 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:UA (auth: p)
Chain Length:113
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH53 Pfam ID:PF00886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:VA (auth: q)
Chain Length:129
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH51 Pfam ID:PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:WA (auth: r)
Chain Length:84
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH49 Pfam ID:PF01084
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:XA (auth: s)
Chain Length:93
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH45 Pfam ID:PF00203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:YA (auth: t)
Chain Length:100
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WH41 Pfam ID:PF01649
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Mitochondrial domain of uncharacterised function (DUF1713)
Chain IDs:ZA (auth: x)
Chain Length:33
Number of Molecules:1
Biological Source:Mycobacterium tuberculosis
UniProt ID:P9WKT5 Pfam ID:PF08213
Primary Citation
Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.
Nucleic Acids Res. 45 10884 10894 (2017)
PMID: 28977617 DOI: 10.1093/nar/gkx785

Abstact

Ribosomes from Mycobacterium tuberculosis (Mtb) possess species-specific ribosomal RNA (rRNA) expansion segments and ribosomal proteins (rProtein). Here, we present the near-atomic structures of the Mtb 50S ribosomal subunit and the complete Mtb 70S ribosome, solved by cryo-electron microscopy. Upon joining of the large and small ribosomal subunits, a 100-nt long expansion segment of the Mtb 23S rRNA, named H54a or the 'handle', switches interactions from with rRNA helix H68 and rProtein uL2 to with rProtein bS6, forming a new intersubunit bridge 'B9'. In Mtb 70S, bridge B9 is mostly maintained, leading to correlated motions among the handle, the L1 stalk and the small subunit in the rotated and non-rotated states. Two new protein densities were discovered near the decoding center and the peptidyl transferase center, respectively. These results provide a structural basis for studying translation in Mtb as well as developing new tuberculosis drugs.

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Disease

Primary Citation of related structures
5V7Q