4HWY | pdb_00004hwy

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

• PDB DOI: https://doi.org/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 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

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: https://doi.org/10.1126/science.1229663
• Primary Citation 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: 
• Joint Laboratory for Structural Biology of Infection and Inflammation, Institute of Biochemistry and Molecular Biology, University of Hamburg, and Institute of Biochemistry, University of Lübeck, at Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany.
German Centre for Infection Research, University of Lübeck, 23538 Lübeck, Germany.
Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120 Heidelberg, Germany.
Max Planck Advanced Study Group, Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Linac Coherent Light Source, Stanford Linear Accelerator Center (SLAC) National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Department of Chemistry and Molecular Biology, University of Gothenburg, SE-405 30 Gothenburg, Sweden.
Photon Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany.
Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany.
Photon Ultrafast Laser Science and Engineering (PULSE) Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA.
Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287, USA.
Department of Physics, Arizona State University, Tempe, AZ 85287, USA.
Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA 94550, USA.
Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, SE-75124 Uppsala, Sweden.
Institute of Biochemistry and Molecular Biology, University of Hamburg, at DESY, Notkestrasse 85, 22607 Hamburg, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 38.27 kDa 
• Atom Count: 2,551 
• Modeled Residue Count: 308 
• Deposited Residue Count: 340 
• Unique protein chains: 1

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
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	Length	2D Diagram	Glycosylation	D Interactions
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 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

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

• 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
• Version 2.1: 2023-09-20
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-09
  Changes: Structure summary