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- PDB-9gj2: Crystal structure of human cathepsin S produced in insect cells i... -

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Basic information

Entry
Database: PDB / ID: 9gj2
TitleCrystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b
ComponentsCathepsin S
KeywordsHYDROLASE / cysteine protease / drug target / thiohemiketal / main protease inhibitor
Function / homology
Function and homology information


cathepsin S / regulation of antigen processing and presentation / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / cellular response to thyroid hormone stimulus / response to acidic pH / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin S / regulation of antigen processing and presentation / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / cellular response to thyroid hormone stimulus / response to acidic pH / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / antigen processing and presentation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / laminin binding / collagen binding / phagocytic vesicle / Degradation of the extracellular matrix / MHC class II antigen presentation / cysteine-type peptidase activity / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / : / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / serine-type endopeptidase activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular space / extracellular region
Similarity search - Function
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 ...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
CITRIC ACID / Chem-KH0 / Cathepsin S
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsFalke, S. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. / Reinke, P.Y.A. / Guenther, S. / Turk, D. / Meents, A.
Funding support Germany, Slovenia, 5items
OrganizationGrant numberCountry
Helmholtz AssociationFISCOV Germany
Helmholtz AssociationSFragX Germany
German Federal Ministry for Education and Research031B0405 Germany
Slovenian Research AgencyP1-0048 Slovenia
Slovenian Research AgencyIO-0048 Slovenia
CitationJournal: To Be Published
Title: Crystal structure of human cathepsin S produced in insect cells in complex with ketoamide 13b
Authors: Falke, S. / Karnicar, K. / Usenik, A. / Lindic, N. / Sekirnik, A. / Reinke, P.Y.A. / Guenther, S. / Turk, D. / Meents, A.
History
DepositionAug 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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 S
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,31011
Polymers53,5222
Non-polymers1,7889
Water8,035446
1
A: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6376
Polymers26,7611
Non-polymers8765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cathepsin S
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6735
Polymers26,7611
Non-polymers9124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.102, 86.102, 152.045
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Space group name HallP4w2c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+3/4
#8: -y,-x,-z+1/4
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cathepsin S


Mass: 26760.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25774, cathepsin S

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Non-polymers , 5 types, 455 molecules

#2: Chemical ChemComp-KH0 / ~{tert}-butyl ~{N}-[1-[(2~{S})-3-cyclopropyl-1-oxidanylidene-1-[[(2~{S},3~{S})-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]-4-[(phenylmethyl)amino]butan-2-yl]amino]propan-2-yl]-2-oxidanylidene-pyridin-3-yl]carbamate / (S,S,S)-13b / ketoamide inhibitor 13b (bound)


Mass: 595.687 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H41N5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 446 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Cathepsin S (7 mg/ml) was mixed with an equal volume of reservoir and equilibrated against 20% (w/v) PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 4.6. Crystals were soaked with ...Details: Cathepsin S (7 mg/ml) was mixed with an equal volume of reservoir and equilibrated against 20% (w/v) PEG4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate pH 4.6. Crystals were soaked with ketoamide 13b in the presence of 5% (v/v) DMSO.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.15→47.52 Å / Num. obs: 353434 / % possible obs: 91.1 % / Redundancy: 11.7 % / CC1/2: 0.999 / Rrim(I) all: 0.083 / Net I/σ(I): 15.22
Reflection shellResolution: 1.15→1.16 Å / Num. unique obs: 4119 / CC1/2: 0.215

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286_9999refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→47.52 Å / SU ML: 0.1078 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1618 3837 1.09 %
Rwork0.1513 349511 -
obs0.1514 353348 91.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.47 Å2
Refinement stepCycle: LAST / Resolution: 1.15→47.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 123 446 3972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00423685
X-RAY DIFFRACTIONf_angle_d0.74484989
X-RAY DIFFRACTIONf_chiral_restr0.0756499
X-RAY DIFFRACTIONf_plane_restr0.0061666
X-RAY DIFFRACTIONf_dihedral_angle_d15.25021375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.3883700.35226157X-RAY DIFFRACTION43.33
1.16-1.180.3275840.31957673X-RAY DIFFRACTION53.79
1.18-1.20.3882960.30058665X-RAY DIFFRACTION60.99
1.2-1.210.29781060.28449685X-RAY DIFFRACTION68.36
1.21-1.230.26251150.251910547X-RAY DIFFRACTION74.3
1.23-1.250.23691270.228511473X-RAY DIFFRACTION80.75
1.25-1.270.1741340.212512303X-RAY DIFFRACTION86.78
1.27-1.290.19471480.194913428X-RAY DIFFRACTION94.45
1.29-1.320.19271490.176413951X-RAY DIFFRACTION98.13
1.32-1.340.18821590.164114105X-RAY DIFFRACTION99.19
1.34-1.370.16941510.15614180X-RAY DIFFRACTION99.65
1.37-1.40.1571540.135714187X-RAY DIFFRACTION99.85
1.4-1.430.12651530.128814213X-RAY DIFFRACTION99.9
1.43-1.470.11361580.12514171X-RAY DIFFRACTION99.91
1.47-1.510.16881560.121414239X-RAY DIFFRACTION99.96
1.51-1.550.15991540.120414200X-RAY DIFFRACTION99.99
1.55-1.60.12881530.121114217X-RAY DIFFRACTION99.99
1.6-1.660.13671580.120514207X-RAY DIFFRACTION100
1.66-1.730.13941590.127714217X-RAY DIFFRACTION99.99
1.73-1.80.17951540.14314203X-RAY DIFFRACTION100
1.8-1.90.1671560.135614211X-RAY DIFFRACTION100
1.9-2.020.13741560.135714175X-RAY DIFFRACTION99.99
2.02-2.170.15781560.139114249X-RAY DIFFRACTION100
2.17-2.390.1761550.149114228X-RAY DIFFRACTION99.99
2.39-2.740.13081550.158114176X-RAY DIFFRACTION100
2.74-3.450.17521620.162614244X-RAY DIFFRACTION100
3.45-47.520.15061590.144614207X-RAY DIFFRACTION99.9

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