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- PDB-3cbk: chagasin-cathepsin B -

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Basic information

Entry
Database: PDB / ID: 3cbk
Titlechagasin-cathepsin B
Components
  • Cathepsin B
  • Chagasin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / chagasin / cathepsin B / occluding loop / Chagas disease / Glycoprotein / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen / Cytoplasmic vesicle / Protease inhibitor / Thiol protease inhibitor / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


ciliary pocket / cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity ...ciliary pocket / cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity / Collagen degradation / decidualization / collagen catabolic process / epithelial cell differentiation / cysteine-type peptidase activity / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / cytoplasmic vesicle / collagen-containing extracellular matrix / regulation of apoptotic process / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Immunoglobulin-like - #2020 / Proteinase inhibitor I42, chagasin / Chagasin-like superfamily / : / Chagasin family peptidase inhibitor I42 / Peptidase C1A, propeptide / Peptidase family C1 propeptide / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site ...Immunoglobulin-like - #2020 / Proteinase inhibitor I42, chagasin / Chagasin-like superfamily / : / Chagasin family peptidase inhibitor I42 / Peptidase C1A, propeptide / Peptidase family C1 propeptide / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cathepsin B / Chagasin
Similarity search - Component
Biological speciesHomo sapiens (human)
Trypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsRedzynia, I. / Bujacz, G.D. / Abrahamson, M. / Ljunggren, A. / Jaskolski, M. / Mort, J.S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Displacement of the occluding loop by the parasite protein, chagasin, results in efficient inhibition of human cathepsin B.
Authors: Redzynia, I. / Ljunggren, A. / Abrahamson, M. / Mort, J.S. / Krupa, J.C. / Jaskolski, M. / Bujacz, G.
History
DepositionFeb 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin B
B: Chagasin


Theoretical massNumber of molelcules
Total (without water)41,3662
Polymers41,3662
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-16.4 kcal/mol
Surface area16140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.066, 85.066, 115.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Cathepsin B / Cathepsin B1 / APP secretase / APPS


Mass: 29311.621 Da / Num. of mol.: 1 / Mutation: C29A, H110A, S115A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P07858, cathepsin B
#2: Protein Chagasin


Mass: 12054.476 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: cha / Plasmid: p-GEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q966X9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN THE CHAIN A, PHE 57P, THR 58P, GLU 59P, ASP 60P, LEU 61P, LYS 62P BELONG TO PROSEGMENT SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.14M ammonium fluoride, 14% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.041 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 20, 2007 / Details: monochromator, multilayer mirror
RadiationMonochromator: bent silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
ReflectionResolution: 2.67→68.52 Å / Num. all: 12662 / Num. obs: 11903 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 69.27 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 15
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 5 % / Rmerge(I) obs: 0.576 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1266 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CBJ

3cbj


Resolution: 2.67→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 19.175 / SU ML: 0.249 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24232 573 4.8 %RANDOM
Rwork0.19311 ---
obs0.19543 11311 94.12 %-
all-12662 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.476 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20 Å2
2--1.39 Å20 Å2
3----2.79 Å2
Refinement stepCycle: LAST / Resolution: 2.67→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 0 63 2883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0212917
X-RAY DIFFRACTIONr_angle_refined_deg2.3571.9273972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0845365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41424.242132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.7915436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7041511
X-RAY DIFFRACTIONr_chiral_restr0.1560.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022282
X-RAY DIFFRACTIONr_nbd_refined0.2640.21421
X-RAY DIFFRACTIONr_nbtor_refined0.3340.21902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2530.2133
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4180.24
X-RAY DIFFRACTIONr_mcbond_it0.9561.51859
X-RAY DIFFRACTIONr_mcangle_it1.60822915
X-RAY DIFFRACTIONr_scbond_it2.49431246
X-RAY DIFFRACTIONr_scangle_it3.7434.51057
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 42 -
Rwork0.264 828 -
obs--95.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.52550.22150.76732.08750.60873.953-0.0687-0.03730.2761-0.1221-0.01990.0324-0.05560.39930.0886-0.3277-0.00530.08650.0586-0.0786-0.062632.675118.220722.4048
21.6037-0.59780.08663.0368-1.492.3883-0.08690.25340.0151-0.15990.04090.2583-0.3234-0.2420.046-0.0097-0.16070.12330.0733-0.1136-0.089424.421143.475710.1906
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA61 - 25567 - 261
2X-RAY DIFFRACTION2BB1 - 1101 - 110

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