5V93

Cryo-EM structure of the 70S ribosome from Mycobacterium tuberculosis bound with Capreomycin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.

Yang, K.Chang, J.Y.Cui, Z.Li, X.Meng, R.Duan, L.Thongchol, J.Jakana, J.Huwe, C.M.Sacchettini, J.C.Zhang, J.

(2017) Nucleic Acids Res 45: 10884-10894

  • DOI: 10.1093/nar/gkx785
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
57Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045IMI5 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IMI5

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
55Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045HU86 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HU86

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
47Mycobacterium tuberculosisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
37Mycobacterium tuberculosisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
217Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045HU18 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HU18

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
152Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045JW48 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JW48

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
147Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A0T9D5H2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0T9D5H2

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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Mycobacterium tuberculosisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
146Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplOERS007688_04067
Find proteins for A0A654TTE7 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A654TTE7

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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
138Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045IWV9 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IWV9

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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
122Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045JK28 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JK28

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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
LSU ribosomal protein L21p
R
104Mycobacterium tuberculosisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
197Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045H760 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045H760

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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
215Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045JAK4 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JAK4

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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Capreomycin
b
6Streptomyces californicusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
274Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045H4H6 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045H4H6

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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
201Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045GRS4 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045GRS4

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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
220Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045JKV0 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JKV0

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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045JMN7 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JMN7

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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
132Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045IWX2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IWX2

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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
139Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045I821 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045I821

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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
61Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045HUG3 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HUG3

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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
162Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045JER3 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JER3

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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
135Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A0E9AP91 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0E9AP91

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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial domain of uncharacterised function (DUF1713)
x
33Mycobacterium tuberculosisMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
223Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
Find proteins for A0A045J9H1 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045J9H1

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Entity ID: 7
MoleculeChainsLengthOrganism
23S rRNAA3138Mycobacterium tuberculosis

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Entity ID: 8
MoleculeChainsLengthOrganism
5S rRNAB115Mycobacterium tuberculosis

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Entity ID: 32
MoleculeChainsLengthOrganism
16S rRNAa1537Mycobacterium tuberculosis
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
DPP
Query on DPP
b
L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
b
L-PEPTIDE LINKINGC6 H14 N2 O2LYS
MYN
Query on MYN
b
L-PEPTIDE LINKINGC6 H12 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-20
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Database references