+Open data
-Basic information
Entry | Database: PDB / ID: 1cjl | ||||||
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Title | CRYSTAL STRUCTURE OF A CYSTEINE PROTEASE PROFORM | ||||||
Components | PROCATHEPSIN L | ||||||
Keywords | HYDROLASE / 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 / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / Collagen degradation / fibronectin binding / antigen processing and presentation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / Attachment and Entry / positive regulation of apoptotic signaling pathway / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / adaptive immune response / lysosome / immune response / symbiont entry into host cell / 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 / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Coulombe, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cjl.cif.gz | 84.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cjl.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 1cjl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cj/1cjl ftp://data.pdbj.org/pub/pdb/validation_reports/cj/1cjl | HTTPS FTP |
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-Related structure data
Related structure data | 1cs8C 1aecS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Water | ChemComp-HOH / |
Sequence details | PROREGION IS NUMBERED FROM 5P TO 96P WITH "P" IN THE RESIDUE INSERTION FIELD (COLUMN #17). |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48 % | |||||||||||||||
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Crystal grow | pH: 7.8 / Details: 1.4M (NA,K)PO4, PH 7.8 | |||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Mar 14, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.2→2.31 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 4 / % possible all: 51.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ACTINIDIN (PDB ENTRY 1AEC) Resolution: 2.2→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 20.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |