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- PDB-2nqd: Crystal structure of cysteine protease inhibitor, chagasin, in co... -

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Basic information

Entry
Database: PDB / ID: 2nqd
TitleCrystal structure of cysteine protease inhibitor, chagasin, in complex with human cathepsin L
Components
  • Cathepsin L
  • Chagasin
KeywordsHYDROLASE INHIBITOR/HYDROLASE / chagasin-cathepsin L complex / three prong inhibition mode / HYDROLASE INHIBITOR-HYDROLASE COMPLEX
Function / homology
Function and homology information


ciliary pocket / enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen ...ciliary pocket / enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / protein autoprocessing / Collagen degradation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / cytoplasmic vesicle / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / lysosome / symbiont entry into host cell / immune response / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane
Similarity search - Function
Immunoglobulin-like - #2020 / Proteinase inhibitor I42, chagasin / Chagasin-like superfamily / Chagasin family peptidase inhibitor I42 / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site ...Immunoglobulin-like - #2020 / Proteinase inhibitor I42, chagasin / Chagasin-like superfamily / Chagasin family peptidase inhibitor I42 / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / 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
Procathepsin L / Chagasin
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRedzynia, I. / Bujacz, G. / Ljunggren, A. / Jaskolski, M. / Abrahamson, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the parasite protease inhibitor chagasin in complex with a host target cysteine protease
Authors: Ljunggren, A. / Redzynia, I. / Alvarez-Fernandez, M. / Abrahamson, M. / Mort, J.S. / Krupa, J.C. / Jaskolski, M. / Bujacz, G.
History
DepositionOct 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 25, 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

Downloads & links

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Assembly

Deposited unit
A: Chagasin
B: Cathepsin L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6955
Polymers36,2122
Non-polymers4833
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-25 kcal/mol
Surface area14940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.270, 50.063, 65.008
Angle α, β, γ (deg.)90.000, 103.440, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Chagasin / cysteine protease inhibitor


Mass: 11923.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q966X9
#2: Protein Cathepsin L / cysteine protease / Major excreted protein / MEP


Mass: 24288.750 Da / Num. of mol.: 1 / Fragment: residues 1-220 / Mutation: C25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPIC9 / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / References: UniProt: P07711, cathepsin L

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 566 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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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: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% iso-Propanol, 20% PEG 4000, 0.1M Na Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8078 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 18, 2005
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8078 Å / Relative weight: 1
ReflectionResolution: 1.74→63.25 Å / Num. all: 37938 / Num. obs: 37521 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 18.975 Å2 / Rmerge(I) obs: 0.061 / Χ2: 1.068 / Net I/σ(I): 12.1
Reflection shellResolution: 1.74→1.81 Å / Redundancy: 3 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3478 / Χ2: 1.427 / % possible all: 92.5

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation1.9 Å39.25 Å
Translation1.9 Å39.25 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NNR, 1CS8

2nnr

1cs8


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.729 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1891 5 %RANDOM
Rwork0.148 ---
all0.151 37938 --
obs0.15 37513 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.463 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 30 564 3142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222769
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9493766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9425332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23825.072138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82515452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0141510
X-RAY DIFFRACTIONr_chiral_restr0.1110.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022146
X-RAY DIFFRACTIONr_nbd_refined0.2040.21299
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2472
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.237
X-RAY DIFFRACTIONr_mcbond_it0.81.51662
X-RAY DIFFRACTIONr_mcangle_it1.39122694
X-RAY DIFFRACTIONr_scbond_it2.15931159
X-RAY DIFFRACTIONr_scangle_it3.4294.51071
LS refinement shellResolution: 1.75→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 103 -
Rwork0.215 2089 -
obs-2192 78.4 %
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)
10.708-0.01840.23450.4409-0.16790.79230.0245-0.0111-0.03360.0035-0.0481-0.02530.06470.08760.0236-0.01750.00940.0072-0.03410.0034-0.025311.1416-0.527411.3592
22.4558-0.67170.04360.3292-0.10950.4045-0.127-0.03590.10110.01480.08260.0352-0.0275-0.07420.0444-0.03230.00290.0002-0.0207-0.0102-0.0154-17.59949.773517.0279
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11BB1 - 2202 - 221
22AA2 - 1101 - 109

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