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

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


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: https://doi.org/10.1126/science.1229663
  • Primary Citation of Related Structures:  

  • 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 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

    Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine peptidase C (CPC)340Trypanosoma brucei brucei TREU927Mutation(s): 0 
Gene Names: Tb927.6.560
EC: 3.4.22
Find proteins for D6XHE1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore D6XHE1 
Go to UniProtKB:  D6XHE1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6XHE1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.4α = 90
b = 125.4β = 90
c = 54.56γ = 90
Software Package:
Software NamePurpose
CXIdata collection
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2012-12-19
    Changes: Database references
  • Version 1.2: 2013-01-23
    Changes: Database references
  • Version 1.3: 2016-12-21
    Changes: Data collection
  • Version 1.4: 2017-11-15
    Changes: Advisory, Data collection
  • Version 1.5: 2018-02-14
    Changes: Data collection, Source and taxonomy
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary