7VMX | pdb_00007vmx

The Crystal Structure of EF-Tu and EF-Ts complex from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.232 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural insights of the elongation factor EF-Tu complexes in protein translation of Mycobacterium tuberculosis.

Zhan, B.Gao, Y.Gao, W.Li, Y.Li, Z.Qi, Q.Lan, X.Shen, H.Gan, J.Zhao, G.Li, J.

(2022) Commun Biol 5: 1052-1052

  • DOI: https://doi.org/10.1038/s42003-022-04019-y
  • Primary Citation Related Structures: 
    7VMX, 7VOK

  • PubMed Abstract: 

    Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second-deadliest infectious disease worldwide. Emerging evidence shows that the elongation factor EF-Tu could be an excellent target for treating Mtb infection. Here, we report the crystal structures of Mtb EF-Tu•EF-Ts and EF-Tu•GDP complexes, showing the molecular basis of EF-Tu's representative recycling and inactive forms in protein translation. Mtb EF-Tu binds with EF-Ts at a 1:1 ratio in solution and crystal packing. Mutation and SAXS analysis show that EF-Ts residues Arg13, Asn82, and His149 are indispensable for the EF-Tu/EF-Ts complex formation. The GDP binding pocket of EF-Tu dramatically changes conformations upon binding with EF-Ts, sharing a similar GDP-exchange mechanism in E. coli and T. ther. Also, the FDA-approved drug Osimertinib inhibits the growth of M. smegmatis, H37Ra, and M. bovis BCG strains by directly binding with EF-Tu. Thus, our work reveals the structural basis of Mtb EF-Tu in polypeptide synthesis and may provide a promising candidate for TB treatment.


  • Organizational Affiliation
    • State Key Laboratory of Genetic Engineering, School of Life Sciences, Shanghai Engineering Research Center of Industrial Microorganisms, Fudan University, 200438, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 72.86 kDa 
  • Atom Count: 4,717 
  • Modeled Residue Count: 619 
  • Deposited Residue Count: 667 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor Ts271Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
UniProt
Find proteins for P9WNM1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNM1 
Go to UniProtKB:  P9WNM1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNM1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongation factor Tu396Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 3.6.5.3
UniProt
Find proteins for P9WNN1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNN1 
Go to UniProtKB:  P9WNN1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNN1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.232 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.114α = 90
b = 128.114β = 90
c = 200.671γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2016YFA0500600

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-12
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-04-24
    Changes: Database references