5V93

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 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
  • Primary Citation of Related Structures:  

  • 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

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
0
57Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmF (rpmF_1, rpmF_2)
Find proteins for A0A045IMI5 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IMI5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
1
55Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmG2 (rpmG, rpmG2_1)
Find proteins for A0A045HU86 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HU86
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
2
47N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
3
64Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmI (rpmI_1, rpmI_2)
Find proteins for A0A045KKY9 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045KKY9
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
4
37N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
6
80Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmE (rpmE_1, rpmE_2)
Find proteins for A0A045HLX7 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HLX7
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
C
280Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplB (rplB_1, rplB_2)
Find proteins for A0A045H5T7 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045H5T7
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
D
217Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplC (rplC_1)
Find proteins for A0A045HU18 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HU18
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
E
223Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplD (rplD_1)
Find proteins for A0A045J9H1 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045J9H1
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
F
187Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplE (rplE_1)
Find proteins for A0A045HUU0 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HUU0
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
G
179Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplF_1 (rplF, rplF_2)
Find proteins for A0A045JJU1 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JJU1
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
H
152Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplI (rplI_2)
Find proteins for A0A045JW48 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JW48
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
J
147Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplM
Find proteins for A0A0T9D5H2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0T9D5H2
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
K
122Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplN
Find proteins for A0A0U0S3A8 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0U0S3A8
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
L
146Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplO
Find proteins for A0A0T7M0A0 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0T7M0A0
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
M
138Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplP (rplP_1, rplP_2)
Find proteins for A0A045IWV9 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IWV9
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
N
180Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplQ (rplQ_1)
Find proteins for A0A045IVA2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IVA2
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
O
122Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplR (rplR_1, rplR_2)
Find proteins for A0A045JK28 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JK28
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
P
113Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplS (rplS_1)
Find proteins for A0A045IDD2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IDD2
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
Q
129Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplT (rplT_1, rplT_2)
Find proteins for A0A045KJ85 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045KJ85
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
LSU ribosomal protein L21p
R
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
S
197Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplV (rplV_1, rplV_2)
Find proteins for A0A045H760 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045H760
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
T
100Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplW (rplW_1)
Find proteins for A0A045J9M3 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045J9M3
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
U
105Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplX (rplX_1, rplX_2)
Find proteins for A0A045IXU4 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IXU4
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
V
215Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rplY (ctc, rplY_1)
Find proteins for A0A045JAK4 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JAK4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
W
86Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmA (rpmA_1, rpmA_2)
Find proteins for A0A045K0G1 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045K0G1
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
X
64Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmB
Find proteins for A0A045IDB8 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IDB8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
Y
77Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmC (rpmC_1, rpmC_2)
Find proteins for A0A045IQ64 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IQ64
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
Z
65Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpmD_1 (rpmD)
Find proteins for A0A045H4J2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045H4J2
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Capreomycin
b
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
c
274Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsC (rpsC_1, rpsC_2)
Find proteins for A0A045H4H6 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045H4H6
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
d
201Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsD_1 (rpsD)
Find proteins for A0A045GRS4 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045GRS4
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
e
220Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsE (rpsE_2)
Find proteins for A0A045JKV0 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JKV0
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
f
96Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsF (rpsF_1, rpsF_2)
Find proteins for A0A045JVY9 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JVY9
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
g
156Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsG (rpsG_1, rpsG_2)
Find proteins for A0A045JMN7 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JMN7
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
h
132Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsH (rpsH_1, rpsH_2)
Find proteins for A0A045IWX2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IWX2
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
i
151Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsI (rpsI_1, rpsI_2)
Find proteins for A0A045I839 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045I839
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
j
101Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsJ (rpsJ_1)
Find proteins for A0A045HTN2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HTN2
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
k
139Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsK
Find proteins for A0A045I821 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045I821
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
l
124Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsL (rpsL_1, rpsL_2)
Find proteins for M9TET4 (Mycobacterium tuberculosis)
Go to UniProtKB:  M9TET4
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
m
124Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsM (rpsM_1)
Find proteins for A0A045GT82 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045GT82
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
n
61Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsN1 (rpsN, rpsZ)
Find proteins for A0A045HUG3 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045HUG3
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
o
89Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsO (rpsO_1)
Find proteins for A0A045JF49 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JF49
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
p
162Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsP (rpsP_1)
Find proteins for A0A045JER3 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JER3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
q
135Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsQ (rpsQ_1, rpsQ_2)
Find proteins for A0A0E9AP91 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0E9AP91
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
r
84Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsR (rpsR_2)
Find proteins for A0A045JW21 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045JW21
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
s
93Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsS (rpsS_1, rpsS_2)
Find proteins for A0A045IXT2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045IXT2
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
t
86Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rpsT (rpsT_1)
Find proteins for A0A045GXQ2 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A045GXQ2
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
Mitochondrial domain of uncharacterised function (DUF1713)
x
33Mycobacterium tuberculosisMutation(s): 0 
Find proteins for A0A0T5Y2Y4 (Mycobacterium tuberculosis)
Go to UniProtKB:  A0A0T5Y2Y4
Entity ID: 7
MoleculeChainsLengthOrganism
23S rRNAA3138Mycobacterium tuberculosis
Entity ID: 8
MoleculeChainsLengthOrganism
5S rRNAB115Mycobacterium tuberculosis
Entity ID: 32
MoleculeChainsLengthOrganism
16S rRNAa1537Mycobacterium tuberculosis
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
MYN
Query on MYN
b
L-peptide linkingC6 H12 N4 O2ARG
UAL
Query on UAL
b
peptide linkingC4 H7 N3 O3

--

DPP
Query on DPP
b
L-PEPTIDE LINKINGC3 H8 N2 O2ALA
KBE
Query on KBE
b
L-peptide linkingC6 H14 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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