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- PDB-3cbj: Chagasin-Cathepsin B complex -

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Basic information

Entry
Database: PDB / ID: 3cbj
TitleChagasin-Cathepsin B complex
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 / cysteine-type peptidase activity / epithelial cell differentiation / 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
PHOSPHATE ION / Cathepsin B / Chagasin
Similarity search - Component
Biological speciesHomo sapiens (human)
Trypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7466
Polymers41,3662
Non-polymers3804
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-35.1 kcal/mol
Surface area15790 Å2
MethodPISA
2
A: Cathepsin B
B: Chagasin
hetero molecules

A: Cathepsin B
B: Chagasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,49212
Polymers82,7324
Non-polymers7608
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8220 Å2
ΔGint-75.7 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.255, 30.778, 79.745
Angle α, β, γ (deg.)90.00, 92.68, 90.00
Int Tables number5
Space group name H-MC121

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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: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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 Å3/Da / Density % sol: 38.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium dihydrogen phosphate, 20% PEG 3350, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 21, 2007 / Details: monochromator + multilayer mirror
RadiationMonochromator: Bent diamond crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907 Å / Relative weight: 1
ReflectionResolution: 1.8→79.56 Å / Num. all: 30961 / Num. obs: 30592 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 18.98 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3096 / % possible all: 97.2

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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 1HUC

1huc


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.349 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(I): -3 / ESU R: 0.13 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20982 1537 5 %RANDOM
Rwork0.16265 ---
obs0.16501 29055 98.74 %-
all-30961 --
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: 26.079 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-1.36 Å2
2---0.04 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 20 243 3084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212955
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9364025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5145366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.9524.135133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54515448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.351512
X-RAY DIFFRACTIONr_chiral_restr0.1170.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022295
X-RAY DIFFRACTIONr_nbd_refined0.2080.21413
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21988
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.218
X-RAY DIFFRACTIONr_mcbond_it1.1151.51858
X-RAY DIFFRACTIONr_mcangle_it1.75522931
X-RAY DIFFRACTIONr_scbond_it2.58531280
X-RAY DIFFRACTIONr_scangle_it3.8334.51091
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 100 -
Rwork0.2 2040 -
obs--95.88 %
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)
11.2036-0.34840.41270.6682-0.18120.7498-0.0395-0.1002-0.05180.04960.05190.0125-0.033-0.0447-0.0125-0.02820.00830.0164-0.0452-0.0027-0.05-21.3696-15.131212.3926
22.56140.36891.27620.54050.35381.8952-0.1375-0.1089-0.023-0.00480.0908-0.1081-0.23240.22280.0466-0.0167-0.0018-0.02670.01370.006-0.02765.05-14.700329.6092
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2557 - 261
2X-RAY DIFFRACTION2BB2 - 1102 - 110

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