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- PDB-1cs8: CRYSTAL STRUCTURE OF PROCATHEPSIN L -

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Basic information

Entry
Database: PDB / ID: 1cs8
TitleCRYSTAL STRUCTURE OF PROCATHEPSIN L
ComponentsHUMAN PROCATHEPSIN L
KeywordsHYDROLASE / PROSEGMENT / PROPEPTIDE / INHIBITION
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
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 / Resolution: 1.8 Å
AuthorsCygler, M. / Coulombe, R.
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: 1998
Title: Structural Basis for Specificity of Papain-Like Cysteine Protease Proregions Toward Their Cognate Enzymes
Authors: Groves, M.R. / Coulombe, R. / Jenkins, J. / Cygler, M.
History
DepositionAug 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4May 2, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.id ..._citation.country / _citation.id / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.citation_id / _citation_author.name
Revision 1.5Nov 3, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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

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Assembly

Deposited unit
A: HUMAN PROCATHEPSIN L


Theoretical massNumber of molelcules
Total (without water)35,9211
Polymers35,9211
Non-polymers00
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.29, 104.29, 85.99
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HUMAN PROCATHEPSIN L


Mass: 35920.973 Da / Num. of mol.: 1 / Mutation: T110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PPIC9 / Production host: Pichia pastoris (fungus) / References: UniProt: P07711, cathepsin L
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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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: 3.76 Å3/Da / Density % sol: 67.26 %
Crystal growTemperature: 293.2 K / Method: microbatch / pH: 7.8
Details: Na,K,Phosphate, pH 7.8, MICROBATCH, temperature 20.2K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.924
DetectorType: ADSC / Detector: CCD / Date: Feb 13, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.924 Å / Relative weight: 1
ReflectionResolution: 1.8→45 Å / Num. all: 151997 / Num. obs: 47257 / % possible obs: 93.9 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.224 / Num. unique all: 3322 / % possible all: 66.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.843refinement
RefinementResolution: 1.8→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Some residues have alternate conformations: G24P, M25P, N26P, E28P, Q73P, N108, K120, I132, S158, M201, H208. Several side-chains have occupancies set to zero or 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 2330 -10% of observations
Rwork0.2066 ---
all-50247 --
obs-46725 92.99 %-
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 0 747 3898
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.375

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