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- PDB-7pk4: Tick salivary cystatin Ricistatin in complex with cathepsin V -

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Basic information

Entry
Database: PDB / ID: 7pk4
TitleTick salivary cystatin Ricistatin in complex with cathepsin V
Components
  • Cathepsin L2
  • Putative salivary cystatin
KeywordsHYDROLASE / Complex / cystatin / tick
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 / MHC class II antigen presentation ...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 / MHC class II antigen presentation / Degradation of the extracellular matrix / 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 / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / extracellular space / extracellular region
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase ...Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / 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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative salivary cystatin / Cathepsin L2
Similarity search - Component
Biological speciesHomo sapiens (human)
Ixodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBusa, M. / Mares, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729European Union
CitationJournal: Cell.Mol.Life Sci. / Year: 2023
Title: Protease-bound structure of Ricistatin provides insights into the mechanism of action of tick salivary cystatins in the vertebrate host.
Authors: Martins, L.A. / Busa, M. / Chlastakova, A. / Kotal, J. / Berankova, Z. / Stergiou, N. / Jmel, M.A. / Schmitt, E. / Chmelar, J. / Mares, M. / Kotsyfakis, M.
History
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin L2
B: Putative salivary cystatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,46110
Polymers36,8902
Non-polymers5718
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.488, 45.322, 58.520
Angle α, β, γ (deg.)90.000, 96.890, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 24138.998 Da / Num. of mol.: 1 / Mutation: C25S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSV, CATL2, CTSL2, CTSU, UNQ268/PRO305 / Production host: Komagataella pastoris (fungus) / References: UniProt: O60911, cathepsin V
#2: Protein Putative salivary cystatin


Mass: 12751.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0K8RMA7

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Non-polymers , 4 types, 193 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.88 %
Description: Aggregates resembling hand-reaped wheat sheaves
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.07 M Ammonium acetate 4.5 18.9% w/v PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 2, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.92→43.91 Å / Num. obs: 23406 / % possible obs: 99.2 % / Redundancy: 3.1 % / CC1/2: 0.991 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.09 / Rrim(I) all: 0.16 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.92-1.972.21.07337215040.320.8281.3620.894
9.01-43.873.20.0437752450.9850.030.05222.198.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3kfq

3kfq


Resolution: 1.92→43.87 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.84 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1153 4.9 %RANDOM
Rwork0.1859 ---
obs0.1878 22253 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.37 Å2 / Biso mean: 27.591 Å2 / Biso min: 8.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.92 Å2
2--1.57 Å20 Å2
3----0.76 Å2
Refinement stepCycle: final / Resolution: 1.92→43.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2277 0 37 188 2502
Biso mean--51.43 35.04 -
Num. residues----298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132382
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182200
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.6513213
X-RAY DIFFRACTIONr_angle_other_deg1.3171.5865071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0375299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63623.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36215377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7791510
X-RAY DIFFRACTIONr_chiral_restr0.0650.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
LS refinement shellResolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 105 -
Rwork0.325 1535 -
all-1640 -
obs--94.09 %

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