3MI0

Crystal Structure of Mycobacterium Tuberculosis Proteasome at 2.2 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the assembly and gate closure mechanisms of the Mycobacterium tuberculosis 20S proteasome.

Li, D.Li, H.Wang, T.Pan, H.Lin, G.Li, H.

(2010) Embo J. --: --

  • DOI: 10.1038/emboj.2010.95
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mtb) possesses a proteasome system analogous to the eukaryotic ubiquitin-proteasome pathway. Mtb requires the proteasome to resist killing by the host immune system. The detailed assembly process and the gating mechanism o ...

    Mycobacterium tuberculosis (Mtb) possesses a proteasome system analogous to the eukaryotic ubiquitin-proteasome pathway. Mtb requires the proteasome to resist killing by the host immune system. The detailed assembly process and the gating mechanism of Mtb proteasome have remained unknown. Using cryo-electron microscopy and X-ray crystallography, we have obtained structures of three Mtb proteasome assembly intermediates, showing conformational changes during assembly, and explaining why the beta-subunit propeptide inhibits rather than promotes assembly. Although the eukaryotic proteasome core particles close their protein substrate entrance gates with different amino terminal peptides of the seven alpha-subunits, it has been unknown how a prokaryotic proteasome might close the gate at the symmetry axis with seven identical peptides. We found in the new Mtb proteasome crystal structure that the gate is tightly sealed by the seven identical peptides taking on three distinct conformations. Our work provides the structural bases for assembly and gating mechanisms of the Mtb proteasome.


    Organizational Affiliation

    Department of Biology, Brookhaven National Laboratory, Upton, NY, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha
A, B, D, F, I, K, M, O, Q, S, U, W, Y, 1
248Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcA
EC: 3.4.25.1
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHU1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta
C, E, G, H, J, L, N, P, R, T, V, X, Z, 2
240Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcB
EC: 3.4.25.1
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHT9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMF
Query on DMF

Download SDF File 
Download CCD File 
1, 2, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
SA6
Query on SA6

Download SDF File 
Download CCD File 
2, C, E, G, H, J, L, N, P, R, T, V, X, Z
(2R,3S,4R)-2-[(S)-(1S)-cyclohex-2-en-1-yl(hydroxy)methyl]-4-ethyl-3-hydroxy-3-methyl-5-oxopyrrolidine-2-carbaldehyde
C15 H23 N O4
HSXZBJZQFUJQNN-FUQNVFFISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 170.374α = 90.00
b = 118.436β = 113.02
c = 195.249γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-04-09 
  • Released Date: 2010-06-23 
  • Deposition Author(s): Li, D., Li, H.

Revision History 

  • Version 1.0: 2010-06-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance