7E3G

Crystal structure of Trypanosoma brucei cathepsin B R91C/T223C mutant in the living cell


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.86 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design of an In-Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament.

Abe, S.Pham, T.T.Negishi, H.Yamashita, K.Hirata, K.Ueno, T.

(2021) Angew Chem Int Ed Engl 60: 12341-12345

  • DOI: https://doi.org/10.1002/anie.202102039
  • Primary Citation of Related Structures:  
    7E3E, 7E3F, 7E3G

  • PubMed Abstract: 

    Protein assemblies can be designed for development of nano-bio materials. This has been achieved by modulating protein-protein interactions. However, fabrication of highly ordered protein assemblies remains challenging. Protein crystals, which have highly ordered arrangements of protein molecules, provide useful source matrices for synthesizing artificial protein assemblies. Here, we describe construction of a supramolecular filament structure by engineering covalent and non-covalent interactions in a protein crystal. Performing in-cell crystallization of Trypanosoma brucei cysteine protease cathepsin B (TbCatB), we achieved a precise arrangement of protein molecules while suppressing random aggregation due to disulfide bonds. We succeeded in synthesizing bundled filament from the crystals by autoxidation of cysteinyl thiols after the isolation of the crystals from living cells.


  • Organizational Affiliation

    School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta 4259-B-55, Midori-ku, Yokohama, 226-8501, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteine peptidase C (CPC)340Trypanosoma brucei brucei TREU927Mutation(s): 2 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD6XHE1
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.86 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.177 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.08α = 90
b = 124.08β = 90
c = 52.96γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHENIXphasing
XDSdata processing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18H05421
Japan Society for the Promotion of Science (JSPS)JapanJP18K05140

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-15
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary