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- PDB-3kse: Unreduced cathepsin L in complex with stefin A -

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Basic information

Entry
Database: PDB / ID: 3kse
TitleUnreduced cathepsin L in complex with stefin A
Components
  • Cathepsin L1
  • Cystatin-A
KeywordsHydrolase/Hydrolase inhibitor / cathepsin / protease-inhibitor complex / stefin / cystatin / papain-like / cysteine protease / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen / Thiol protease inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / peptidase inhibitor complex / macrophage apoptotic process / chromaffin granule / elastin catabolic process / peptide cross-linking / antigen processing and presentation of peptide antigen / Formation of the cornified envelope ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / peptidase inhibitor complex / macrophage apoptotic process / chromaffin granule / elastin catabolic process / peptide cross-linking / antigen processing and presentation of peptide antigen / Formation of the cornified envelope / cornified envelope / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / zymogen activation / Assembly of collagen fibrils and other multimeric structures / antigen processing and presentation / protein autoprocessing / Collagen degradation / collagen catabolic process / fibronectin binding / serpin family protein binding / cysteine-type endopeptidase inhibitor activity / keratinocyte differentiation / collagen binding / Attachment and Entry / Degradation of the extracellular matrix / receptor-mediated endocytosis of virus by host cell / negative regulation of proteolysis / multivesicular body / endocytic vesicle lumen / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / cell-cell adhesion / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / protease binding / histone binding / adaptive immune response / Attachment and Entry / lysosome / 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 / symbiont entry into host cell / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / 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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Cystatin-A / Procathepsin L
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsRenko, M. / Turk, D.
CitationJournal: To be Published
Title: Unreduced cathepsin L in complex with stefin A
Authors: Renko, M. / Turk, D.
History
DepositionNov 22, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cathepsin L1
B: Cathepsin L1
C: Cathepsin L1
D: Cystatin-A
E: Cystatin-A
F: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)105,6886
Polymers105,6886
Non-polymers00
Water20,5911143
1
A: Cathepsin L1
D: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)35,2292
Polymers35,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-14 kcal/mol
Surface area14040 Å2
MethodPISA
2
B: Cathepsin L1
E: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)35,2292
Polymers35,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-13 kcal/mol
Surface area14170 Å2
MethodPISA
3
C: Cathepsin L1
F: Cystatin-A


Theoretical massNumber of molelcules
Total (without water)35,2292
Polymers35,2292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint-14 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.233, 83.948, 83.906
Angle α, β, γ (deg.)118.07, 98.04, 98.04
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cathepsin L1 / Major excreted protein / MEP / Cathepsin L1 heavy chain / Cathepsin L1 light chain


Mass: 24208.754 Da / Num. of mol.: 3 / Mutation: T110A,N179D
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
#2: Protein Cystatin-A / Cystatin-AS / Stefin-A


Mass: 11020.464 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01040
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1143 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCATHEPSIN L WAS BLOCKED WITH MMTS (METHYL METHANETHIOSULFONATE), LEAVING -S-CH3 ATOMS ON ACTIVE ...CATHEPSIN L WAS BLOCKED WITH MMTS (METHYL METHANETHIOSULFONATE), LEAVING -S-CH3 ATOMS ON ACTIVE SITE CYSTEINE RESIDUE.

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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: 1.99 Å3/Da / Density % sol: 38.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Tris-HCl, 16% PEG3000, pH 7.0, 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 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2008 / Details: Collimating and focusing, Pt-coated mirrors
RadiationMonochromator: Double Crystal Si111 or White Beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. all: 90358 / Num. obs: 86021 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.3
Reflection shellResolution: 1.69→1.72 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.273 / Num. unique all: 2830 / % possible all: 62.7

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Processing

Software
NameClassification
MAR345dtbdata collection
AMoREphasing
MAINrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KFQ, 1ICF

3kfq

1icf


Resolution: 1.71→15.33 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.204 4292 -RANDOM
Rwork0.153 ---
all0.16 84507 --
obs0.155 84507 100 %-
Displacement parametersBiso mean: 18.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0.04 Å2-0.15 Å2
2---0.19 Å2-0.09 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 1.71→15.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7416 0 0 1143 8559
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.025
X-RAY DIFFRACTIONo_angle_deg2.184
LS refinement shellResolution: 1.706→1.75 Å
RfactorNum. reflection% reflection
Rfree0.282 240 -
Rwork0.218 --
obs--100 %

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