7MU0 | pdb_00007mu0

MtbEttA in the ADP bound state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis.

Cui, Z.Li, X.Shin, J.Gamper, H.Hou, Y.M.Sacchettini, J.C.Zhang, J.

(2022) Nat Commun 13: 432-432

  • DOI: https://doi.org/10.1038/s41467-022-28078-1
  • Primary Citation Related Structures: 
    7MSC, 7MSH, 7MSM, 7MSZ, 7MT2, 7MT3, 7MT7, 7MU0

  • PubMed Abstract: 

    EttA, energy-dependent translational throttle A, is a ribosomal factor that gates ribosome entry into the translation elongation cycle. A detailed understanding of its mechanism of action is limited due to the lack of high-resolution structures along its ATPase cycle. Here we present the cryo-electron microscopy (cryo-EM) structures of EttA from Mycobacterium tuberculosis (Mtb), referred to as MtbEttA, in complex with the Mtb 70S ribosome initiation complex (70SIC) at the pre-hydrolysis (ADPNP) and transition (ADP-VO 4 ) states, and the crystal structure of MtbEttA alone in the post-hydrolysis (ADP) state. We observe that MtbEttA binds the E-site of the Mtb 70SIC, remodeling the P-site tRNA and the ribosomal intersubunit bridge B7a during the ribosomal ratcheting. In return, the rotation of the 30S causes conformational changes in MtbEttA, forcing the two nucleotide-binding sites (NBSs) to alternate to engage each ADPNP in the pre-hydrolysis states, followed by complete engagements of both ADP-VO 4 molecules in the ATP-hydrolysis transition states. In the post-hydrolysis state, the conserved ATP-hydrolysis motifs of MtbEttA dissociate from both ADP molecules, leaving two nucleotide-binding domains (NBDs) in an open conformation. These structures reveal a dynamic interplay between MtbEttA and the Mtb ribosome, providing insights into the mechanism of translational regulation by EttA-like proteins.


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

Macromolecule Content 

  • Total Structure Weight: 125.75 kDa 
  • Atom Count: 8,685 
  • Modeled Residue Count: 1,098 
  • Deposited Residue Count: 1,116 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Energy-dependent translational throttle protein EttA
A, B
558Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: ettARv2477c
EC: 3.6.1
UniProt
Find proteins for P9WQK3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQK3 
Go to UniProtKB:  P9WQK3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQK3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
G [auth B],
H [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth B],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.246 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.06α = 90
b = 106.96β = 90
c = 269.19γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI095208
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU24GM116787

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description