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- PDB-1cjl: CRYSTAL STRUCTURE OF A CYSTEINE PROTEASE PROFORM -

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Basic information

Entry
Database: PDB / ID: 1cjl
TitleCRYSTAL STRUCTURE OF A CYSTEINE PROTEASE PROFORM
ComponentsPROCATHEPSIN L
KeywordsHYDROLASE / PROPEPTIDE / INHIBITOR / CYSTEINE PROTEASE
Function / homology
Function and homology information


enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / 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 / collagen binding / Attachment and Entry / Degradation of the extracellular matrix / receptor-mediated endocytosis of virus by host cell / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / : / 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 / nucleus / plasma membrane
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 proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCoulombe, R. / Grochulski, P. / Sivaraman, J. / Cygler, M.
Citation
Journal: EMBO J. / Year: 1996
Title: Structure of human procathepsin L reveals the molecular basis of inhibition by the prosegment.
Authors: Coulombe, R. / Grochulski, P. / Sivaraman, J. / Menard, R. / Mort, J.S. / Cygler, M.
#1: Journal: Proteins / Year: 1996
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Human Procathepsin L
Authors: Coulombe, R. / Li, Y. / Takebe, S. / Menard, R. / Mason, P. / Mort, J.S. / Cygler, M.
History
DepositionJul 24, 1996Processing site: BNL
Revision 1.0Aug 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROCATHEPSIN L


Theoretical massNumber of molelcules
Total (without water)35,3181
Polymers35,3181
Non-polymers00
Water1,27971
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.080, 88.090, 94.930
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 PROCATHEPSIN L


Mass: 35318.316 Da / Num. of mol.: 1 / Mutation: F(78P)L, C25S, T110A, E176G, D178G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: FIRST RESIDUE (THR) CHANGED TO SER / Gene: HUMAN CDNA / Plasmid: PPIC9 / Gene (production host): HUMAN CDNA / Production host: Pichia pastoris (fungus) / References: UniProt: P07711, cathepsin L
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsPROREGION IS NUMBERED FROM 5P TO 96P WITH "P" IN THE RESIDUE INSERTION FIELD (COLUMN #17).

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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: 2.35 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.8 / Details: 1.4M (NA,K)PO4, PH 7.8
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-3 mg/mlprotein1drop
21.3-1.4 Mphosphate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 14, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40.79 Å / Num. obs: 13872 / % possible obs: 77.9 % / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 8.2
Reflection shellResolution: 2.2→2.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 4 / % possible all: 51.3

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Processing

Software
NameVersionClassification
WEISSdata collection
CCP4data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ACTINIDIN (PDB ENTRY 1AEC)

1aec


Resolution: 2.2→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.241 1332 10 %
Rwork0.182 --
obs0.182 13129 75.9 %
Displacement parametersBiso mean: 20.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 0 71 2516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.179
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it3
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rfree0.297 98 10 %
Rwork0.242 944 -
obs--49.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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