4HWY

Trypanosoma brucei procathepsin B solved from 40 fs free-electron laser pulse data by serial femtosecond X-ray crystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Natively inhibited Trypanosoma brucei cathepsin B structure determined by using an X-ray laser.

Redecke, L.Nass, K.DePonte, D.P.White, T.A.Rehders, D.Barty, A.Stellato, F.Liang, M.Barends, T.R.Boutet, S.Williams, G.J.Messerschmidt, M.Seibert, M.M.Aquila, A.Arnlund, D.Bajt, S.Barth, T.Bogan, M.J.Caleman, C.Chao, T.C.Doak, R.B.Fleckenstein, H.Frank, M.Fromme, R.Galli, L.Grotjohann, I.Hunter, M.S.Johansson, L.C.Kassemeyer, S.Katona, G.Kirian, R.A.Koopmann, R.Kupitz, C.Lomb, L.Martin, A.V.Mogk, S.Neutze, R.Shoeman, R.L.Steinbrener, J.Timneanu, N.Wang, D.Weierstall, U.Zatsepin, N.A.Spence, J.C.Fromme, P.Schlichting, I.Duszenko, M.Betzel, C.Chapman, H.N.

(2013) Science 339: 227-230

  • DOI: 10.1126/science.1229663

  • PubMed Abstract: 
  • The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure ...

    The Trypanosoma brucei cysteine protease cathepsin B (TbCatB), which is involved in host protein degradation, is a promising target to develop new treatments against sleeping sickness, a fatal disease caused by this protozoan parasite. The structure of the mature, active form of TbCatB has so far not provided sufficient information for the design of a safe and specific drug against T. brucei. By combining two recent innovations, in vivo crystallization and serial femtosecond crystallography, we obtained the room-temperature 2.1 angstrom resolution structure of the fully glycosylated precursor complex of TbCatB. The structure reveals the mechanism of native TbCatB inhibition and demonstrates that new biomolecular information can be obtained by the "diffraction-before-destruction" approach of x-ray free-electron lasers from hundreds of thousands of individual microcrystals.


    Organizational Affiliation

    Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of L├╝beck, at Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cysteine peptidase C (CPC)
A
340Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 0 
EC: 3.4.22.-
Find proteins for D6XHE1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  D6XHE1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 125.400α = 90.00
b = 125.400β = 90.00
c = 54.560γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing
REFMACrefinement
CXIdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2012-12-19
    Type: Database references
  • Version 1.2: 2013-01-23
    Type: Database references
  • Version 1.3: 2016-12-21
    Type: Data collection
  • Version 1.4: 2017-11-15
    Type: Advisory, Data collection
  • Version 1.5: 2018-02-14
    Type: Data collection, Source and taxonomy