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- PDB-3h6s: Structure of clitocypin - cathepsin V complex -

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Basic information

Entry
Database: PDB / ID: 3h6s
TitleStructure of clitocypin - cathepsin V complex
Components
  • Cathepsin L2
  • Clitocypin analog
KeywordsHYDROLASE/HYDROLASE INHIBITOR / cathepsin / clitocypin / Kunitz inhibitor / cysteine protease / Disulfide bond / Glycoprotein / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway ...cathepsin V / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / extracellular matrix disassembly / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / MHC class II antigen presentation / Degradation of the extracellular matrix / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / extracellular space / extracellular region
Similarity search - Function
Proteinase inhibitor I48, clitocypin / Peptidase inhibitor clitocypin / 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 ...Proteinase inhibitor I48, clitocypin / Peptidase inhibitor clitocypin / 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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cathepsin L2 / Clitocypin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Clitocybe nebularis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsRenko, M. / Sabotic, J. / Brzin, J. / Turk, D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Versatile loops in mycocypins inhibit three protease families.
Authors: Renko, M. / Sabotic, J. / Mihelic, M. / Brzin, J. / Kos, J. / Turk, D.
History
DepositionApr 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 21, 2016Group: Structure summary
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Revision 1.4Oct 13, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin L2
B: Cathepsin L2
C: Cathepsin L2
D: Cathepsin L2
E: Clitocypin analog
F: Clitocypin analog
G: Clitocypin analog
H: Clitocypin analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,58314
Polymers164,0078
Non-polymers5766
Water15,439857
1
A: Cathepsin L2
E: Clitocypin analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0983
Polymers41,0022
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-23 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Cathepsin L2
F: Clitocypin analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2905
Polymers41,0022
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-47 kcal/mol
Surface area16010 Å2
MethodPISA
3
C: Cathepsin L2
G: Clitocypin analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0983
Polymers41,0022
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-23 kcal/mol
Surface area15980 Å2
MethodPISA
4
D: Cathepsin L2
H: Clitocypin analog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0983
Polymers41,0022
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-22 kcal/mol
Surface area16240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.180, 177.760, 96.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is one complex between cathepsin V and clitocypin.

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Components

#1: Protein
Cathepsin L2 / / Cathepsin V / Cathepsin U


Mass: 24087.053 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL2, CATL2, CTSU, CTSV, UNQ268/PRO305 / Production host: Pichia pastoris (fungus) / References: UniProt: O60911, cathepsin V
#2: Protein
Clitocypin analog


Mass: 16914.688 Da / Num. of mol.: 4 / Mutation: I82M, L89M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clitocybe nebularis (fungus) / Gene: clt5 / Production host: Pichia pastoris (fungus) / References: UniProt: Q3Y9I6
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 857 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUE 25(CYC) IN CATHEPSIN L2 IS MODIFIED. CATHEPSIN L2 WAS TREATED WITH METHYL ...RESIDUE 25(CYC) IN CATHEPSIN L2 IS MODIFIED. CATHEPSIN L2 WAS TREATED WITH METHYL METHANETHIOSULFONATE (MMTS) TO FORM SCH (S-METHYL-THIO-CYSTEINE).

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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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 0
Details: 0.4 M Li2SO4, 12% PEG800, 20% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 20, 2008
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 81809 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rmerge(I) obs: 0.037 / Χ2: 0.709 / Net I/σ(I): 43.89
Reflection shellResolution: 2.22→2.26 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.171 / Num. unique all: 3148 / Χ2: 0.94 / % possible all: 76.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
AMoREphasing
MAINrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→50 Å / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.839 / SU R Cruickshank DPI: 0.273 / SU Rfree: 0.218 / Isotropic thermal model: random / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4054 -random
Rwork0.182 ---
all0.207 81809 --
obs-81809 98.8 %-
Displacement parametersBiso max: 95.66 Å2 / Biso mean: 32.282 Å2 / Biso min: 3.56 Å2
Refinement stepCycle: LAST / Resolution: 2.22→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11500 0 30 857 12387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.947
X-RAY DIFFRACTIONo_bond_d0.022
LS refinement shellResolution: 2.22→2.26 Å
RfactorNum. reflection
Rfree0.303 400
Rwork0.213 -
obs-7882

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