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- PDB-8hen: Crystal structure of CTSB in complex with 212-148 -

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Basic information

Entry
Database: PDB / ID: 8hen
TitleCrystal structure of CTSB in complex with 212-148
ComponentsCathepsin B
KeywordsANTIVIRAL PROTEIN/INHIBITOR / inhibitor / antiviral / protease / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization ...cathepsin B / peptidase inhibitor complex / thyroid hormone generation / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / Collagen degradation / decidualization / collagen catabolic process / cysteine-type peptidase activity / epithelial cell differentiation / collagen binding / MHC class II antigen presentation / proteolysis involved in protein catabolic process / melanosome / peptidase activity / regulation of apoptotic process / collagen-containing extracellular matrix / ficolin-1-rich granule lumen / lysosome / symbiont entry into host cell / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / Neutrophil degranulation / perinuclear region of cytoplasm / proteolysis / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Peptidase C1A, propeptide / Peptidase family C1 propeptide / : / 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 ...Peptidase C1A, propeptide / Peptidase family C1 propeptide / : / 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
Chem-L4F / Cathepsin B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, H. / Li, D. / Sun, L. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)92169109 China
CitationJournal: Nat Commun / Year: 2023
Title: Structure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry.
Authors: Wang, H. / Yang, Q. / Liu, X. / Xu, Z. / Shao, M. / Li, D. / Duan, Y. / Tang, J. / Yu, X. / Zhang, Y. / Hao, A. / Wang, Y. / Chen, J. / Zhu, C. / Guddat, L. / Chen, H. / Zhang, L. / Chen, X. ...Authors: Wang, H. / Yang, Q. / Liu, X. / Xu, Z. / Shao, M. / Li, D. / Duan, Y. / Tang, J. / Yu, X. / Zhang, Y. / Hao, A. / Wang, Y. / Chen, J. / Zhu, C. / Guddat, L. / Chen, H. / Zhang, L. / Chen, X. / Jiang, B. / Sun, L. / Rao, Z. / Yang, H.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathepsin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2315
Polymers28,2001
Non-polymers1,0304
Water2,504139
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)31.477, 81.597, 94.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cathepsin B / APP secretase / APPS / Cathepsin B1


Mass: 28200.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSB, CPSB / Production host: Escherichia coli (E. coli) / References: UniProt: P07858, cathepsin B
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-L4F / 2-[4-[[(2~{S})-1-oxidanylidene-3-phenyl-1-[[(3~{S})-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]amino]propan-2-yl]carbamoyl]piperazin-1-yl]ethyl 4-carbamimidamidobenzoate


Mass: 767.936 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C41H49N7O6S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M NaAc pH 5.2, 28% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→37.47 Å / Num. obs: 18398 / % possible obs: 99.5 % / Redundancy: 6.09 % / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.162 / Net I/σ(I): 12.19
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.95-2.070.87128540.8390.9741
2.07-2.210.7227380.8840.7951
2.21-2.390.54525820.9420.5921
2.39-2.610.42523780.9550.4621
2.61-2.920.24121650.9790.2621
2.92-3.370.12719190.9920.1381
3.37-4.120.06916570.9970.0751
4.12-5.790.0513080.9980.0551
5.79-37.470.0427970.9990.0471

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Processing

Software
NameVersionClassification
XDS2020-12-02data scaling
PHENIX1.20.1-4487-000refinement
XDS2020-12-02data reduction
PHENIX1.20.1-4487-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6AY2

6ay2


Resolution: 1.95→37.47 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.88 / Phase error: 22.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2315 1837 9.99 %
Rwork0.1854 --
obs0.1901 18380 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→37.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 71 139 2152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082079
X-RAY DIFFRACTIONf_angle_d0.9672826
X-RAY DIFFRACTIONf_dihedral_angle_d16.302725
X-RAY DIFFRACTIONf_chiral_restr0.065278
X-RAY DIFFRACTIONf_plane_restr0.008370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.38681330.28181186X-RAY DIFFRACTION97
2-2.060.26281380.26241245X-RAY DIFFRACTION99
2.06-2.130.30261390.23181244X-RAY DIFFRACTION99
2.13-2.20.3021390.22641252X-RAY DIFFRACTION100
2.2-2.290.24341400.211256X-RAY DIFFRACTION100
2.29-2.40.28091400.19831276X-RAY DIFFRACTION100
2.4-2.520.24981380.20221251X-RAY DIFFRACTION100
2.52-2.680.24371410.19671271X-RAY DIFFRACTION100
2.68-2.890.23871420.18631271X-RAY DIFFRACTION100
2.89-3.180.2381440.19271291X-RAY DIFFRACTION100
3.18-3.640.21791430.16411290X-RAY DIFFRACTION100
3.64-4.580.17091470.14521322X-RAY DIFFRACTION100
4.59-37.470.20821530.17031388X-RAY DIFFRACTION99

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