Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 38.27 kDa 
• Atom Count: 2551 
• Modelled Residue Count: 308 
• Deposited Residue Count: 340 
• Unique protein chains: 1

4HWY

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

• PDB DOI: 10.2210/pdb4HWY/pdb

• Classification: HYDROLASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-11-09 Released: 2012-12-05 
• Deposition Author(s): Redecke, L., Nass, K., DePonte, D.P., White, T.A., Rehders, D., Barty, A., Stellato, F., Liang, M., Barends, T.R.M., Boutet, S., Williams, G.W., 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., Shoemann, R.L., Steinbrener, J., Timneanu, N., Wang, D., Weierstall, U., Zatsepin, N.A., Spence, J.C.H., Fromme, P., Schlichting, I., Duszenko, M., Betzel, C., Chapman, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.213 
• R-Value Work: 0.182 
• R-Value Observed: 0.183 

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

• PubMed: 23196907 
• DOI: 10.1126/science.1229663
• Primary Citation of Related Structures:  
  4HWY


• 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.

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Organizational Affiliation: 

Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine peptidase C (CPC)	A	340	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb927.6.560 EC: 3.4.22
UniProt
Find proteins for D6XHE1 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore D6XHE1  Go to UniProtKB:  D6XHE1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 125.4	α = 90
b = 125.4	β = 90
c = 54.56	γ = 90

Software Package:

Software Name	Purpose
CXI	data collection
MOLREP	phasing
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-11-09 
• Released Date: 2012-12-05 
Deposition Author(s): Redecke, L., Nass, K., DePonte, D.P., White, T.A., Rehders, D., Barty, A., Stellato, F., Liang, M., Barends, T.R.M., Boutet, S., Williams, G.W., 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., Shoemann, R.L., Steinbrener, J., Timneanu, N., Wang, D., Weierstall, U., Zatsepin, N.A., Spence, J.C.H., Fromme, P., Schlichting, I., Duszenko, M., Betzel, C., Chapman, H.

Revision History  

• 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