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- PDB-3f75: Activated Toxoplasma gondii cathepsin L (TgCPL) in complex with i... -

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Basic information

Entry
Database: PDB / ID: 3f75
TitleActivated Toxoplasma gondii cathepsin L (TgCPL) in complex with its propeptide
Components
  • Cathepsin L Propeptide
  • Cathepsin L Protease
KeywordsHYDROLASE / MEDICAL STRUCTURAL GENOMICS OF PATHOGENIC PROTOZOA / MSGPP / cysteine protease / parasite / protozoa / Thiol protease
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space / membrane
Similarity search - Function
Helix Hairpins - #2250 / 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. / : ...Helix Hairpins - #2250 / 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 / Helix Hairpins / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Cathepsin CPL
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsLarson, E.T. / Merritt, E.A. / Medical Structural Genomics of Pathogenic Protozoa (MSGPP)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Toxoplasma gondii cathepsin L is the primary target of the invasion-inhibitory compound morpholinurea-leucyl-homophenyl-vinyl sulfone phenyl.
Authors: Larson, E.T. / Parussini, F. / Huynh, M.H. / Giebel, J.D. / Kelley, A.M. / Zhang, L. / Bogyo, M. / Merritt, E.A. / Carruthers, V.B.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Jul 31, 2013Group: Non-polymer description
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L Protease
P: Cathepsin L Propeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4366
Polymers37,2232
Non-polymers2134
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-13.9 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.621, 65.621, 149.772
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-481-

HOH

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Components

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Protein , 2 types, 2 molecules AP

#1: Protein Cathepsin L Protease / Toxopain-2


Mass: 24428.521 Da / Num. of mol.: 1 / Fragment: UNP residues 199-422
Source method: isolated from a genetically manipulated source
Details: expressed together with chain P as procathepsin L and autoactivated but propeptide not purified from active protease prior to crystallization; structure is a complex of the active protease ...Details: expressed together with chain P as procathepsin L and autoactivated but propeptide not purified from active protease prior to crystallization; structure is a complex of the active protease and its propeptide, labeled as chain A and chain P, respectively, to indicate that they are distinct polypeptide chains
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: CPL / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q6DMN0, cathepsin L
#2: Protein Cathepsin L Propeptide / Toxopain-2


Mass: 12794.354 Da / Num. of mol.: 1 / Fragment: UNP residues 105-198
Mutation: N-terminal His tag replaced all but the last 94 residues of the propeptide domain
Source method: isolated from a genetically manipulated source
Details: N-terminal His tag replaced all but the last 94 residues of the propeptide domain; expressed together with chain A as procathepsin L and autoactivated but propeptide not purified from active ...Details: N-terminal His tag replaced all but the last 94 residues of the propeptide domain; expressed together with chain A as procathepsin L and autoactivated but propeptide not purified from active protease prior to crystallization; structure is a complex of the active protease and its propeptide, labeled as chain A and chain P, respectively, to indicate that they are distinct polypeptide chains
Source: (gene. exp.) Toxoplasma gondii (eukaryote) / Strain: RH / Gene: CPL / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: Q6DMN0, cathepsin L

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Non-polymers , 4 types, 169 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence details1. THE TARGETDB ID FOR THIS PROTEIN WAS NOT AVAILABLE AT THE TIME OF DEPOSITION. 2. THIS ENTRY IS A ...1. THE TARGETDB ID FOR THIS PROTEIN WAS NOT AVAILABLE AT THE TIME OF DEPOSITION. 2. THIS ENTRY IS A COMPLEX OF THE ACTIVE PROTEASE AND ITS PROPEPTIDE, LABELED AS CHAIN A AND CHAIN P, RESPECTIVELY, TO INDICATE THAT THEY ARE DISTINCT POLYPEPTIDE CHAINS. 3. ENTITY 1 (CHAIN A): EXPRESSED TOGETHER WITH CHAIN P AS PROCATHEPSIN L AND AUTOACTIVATED, BUT PROPEPTIDE NOT PURIFIED FROM ACTIVE PROTEASE PRIOR TO CRYSTALLIZATION. 4. ENTITY 2 (CHAIN P): N-TERMINAL HIS TAG REPLACED ALL BUT THE LAST 94 RESIDUES OF THE PROPEPTIDE DOMAIN. EXPRESSED TOGETHER WITH CHAIN A AS PROCATHEPSIN L AND AUTOACTIVATED, BUT PROPEPTIDE NOT PURIFIED FROM ACTIVE PROTEASE PRIOR TO CRYSTALLIZATION.

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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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 40% PEG 8000, 0.1M Ammonium bromide, 0.1M Sodium citrate pH 4.0. Cryoprotected with ~10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 19, 2008
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. all: 23266 / Num. obs: 23266 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.122 / Χ2: 1.026 / Net I/σ(I): 18.128
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2242 / Χ2: 1.031 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.41 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.99 Å
Translation2.5 Å33.99 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.5.0047refinement
PDB_EXTRACT3.006data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CS8 (protease domain only)

1cs8


Resolution: 1.99→33.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 7.38 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20557 1186 5.1 %RANDOM
Rwork0.16538 ---
obs0.16739 23178 99.89 %-
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: 16.904 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.43 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.99→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 7 165 2517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212433
X-RAY DIFFRACTIONr_bond_other_d0.0010.021697
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9393272
X-RAY DIFFRACTIONr_angle_other_deg1.1873.0044094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5425298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75224.016122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7571515
X-RAY DIFFRACTIONr_chiral_restr0.070.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02527
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.69541478
X-RAY DIFFRACTIONr_mcbond_other0.5414615
X-RAY DIFFRACTIONr_mcangle_it2.58162347
X-RAY DIFFRACTIONr_scbond_it3.2996955
X-RAY DIFFRACTIONr_scangle_it4.95810925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.04 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 88 -
Rwork0.22 1563 -
all0.224 1659 -
obs-1651 99.52 %
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)
15.0141.59761.35420.69990.22085.0691-0.0945-0.50170.56220.19-0.1610.1737-0.4786-0.15120.25550.26190.0389-0.01380.1317-0.02120.091730.85110.38960.653
21.05260.1041-0.13361.3822-0.01571.54530.03240.02460.0664-0.00760.0210.304-0.073-0.3475-0.05350.02150.05420.00010.16220.01320.118115.73414.43439.828
36.592-1.8504-0.1472.75291.41733.1360.1644-0.1850.6250.1134-0.17250.0124-0.2436-0.07310.0080.14880.0360.03090.1369-0.03420.099430.08921.07855.67
40.72210.1182-0.2211.1040.01261.271-0.0062-0.0874-0.00040.0968-0.0102-0.0264-0.04170.02690.01640.07520.0254-0.00280.109-0.00320.087835.99913.12344.892
511.2111.3313-3.31026.1258-0.35055.1838-0.0013-0.2859-0.1586-0.0530.0052-0.84920.1250.7099-0.00390.15340.0367-0.01730.1255-0.01230.12244.436-1.03319.43
62.3824-0.69440.23520.9804-0.64455.29340.04010.19070.02960.0164-0.0876-0.1766-0.13390.31210.04750.0967-0.0088-0.02460.1008-0.00240.053135.2126.99514.27
71.191-0.16181.23360.8015-0.46494.0785-0.04080.0644-0.0524-0.03930.0181-0.10150.01350.2810.02270.08630.01070.00090.115-0.00540.070544.9526.78329.212
84.8934-1.0971-3.05073.81760.87323.8077-0.01950.0190.209-0.15730.10670.2228-0.3245-0.2929-0.08720.07270.0325-0.03860.12460.01890.080832.37819.5629.243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 15
2X-RAY DIFFRACTION2A16 - 118
3X-RAY DIFFRACTION3A119 - 135
4X-RAY DIFFRACTION4A136 - 224
5X-RAY DIFFRACTION5P108 - 123
6X-RAY DIFFRACTION6P124 - 136
7X-RAY DIFFRACTION7P137 - 168
8X-RAY DIFFRACTION8P169 - 182

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