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- PDB-1k3b: Crystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): ... -

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Basic information

Entry
Database: PDB / ID: 1k3b
TitleCrystal Structure of Human Dipeptidyl Peptidase I (Cathepsin C): Exclusion Domain Added to an Endopeptidase Framework Creates the Machine for Activation of Granular Serine Proteases
Components(dipeptydil-peptidase I ...) x 3
KeywordsHYDROLASE
Function / homology
Function and homology information


dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / COPII-coated ER to Golgi transport vesicle / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / phosphatase binding / endoplasmic reticulum-Golgi intermediate compartment membrane / MHC class II antigen presentation / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / azurophil granule lumen / protein-folding chaperone binding / : / lysosome / immune response / endoplasmic reticulum lumen / serine-type endopeptidase activity / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane
Similarity search - Function
Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. ...Cathepsin C, exclusion domain / Cysteine proteinases. Chain C / Cathepsin C exclusion / Cathepsin C, exclusion domain superfamily / Cathepsin C / Cathepsin C exclusion domain / 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 / Lipocalin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Alpha-Beta Complex / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Dipeptidyl peptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MIR, MOL. REPL together / Resolution: 2.15 Å
AuthorsTurk, D. / Janjic, V. / Stern, I. / Podobnik, M. / Lamba, D. / Dahl, S.W. / Lauritzen, C. / Pedersen, J. / Turk, V. / Turk, B.
CitationJournal: EMBO J. / Year: 2001
Title: Structure of human dipeptidyl peptidase I (cathepsin C): exclusion domain added to an endopeptidase framework creates the machine for activation of granular serine proteases.
Authors: Turk, D. / Janjic, V. / Stern, I. / Podobnik, M. / Lamba, D. / Dahl, S.W. / Lauritzen, C. / Pedersen, J. / Turk, V. / Turk, B.
History
DepositionOct 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / software / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dipeptydil-peptidase I exclusion domain
B: dipeptydil-peptidase I light chain
C: dipeptydil-peptidase I heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1208
Polymers39,5753
Non-polymers5455
Water8,359464
1
A: dipeptydil-peptidase I exclusion domain
B: dipeptydil-peptidase I light chain
C: dipeptydil-peptidase I heavy chain
hetero molecules

A: dipeptydil-peptidase I exclusion domain
B: dipeptydil-peptidase I light chain
C: dipeptydil-peptidase I heavy chain
hetero molecules

A: dipeptydil-peptidase I exclusion domain
B: dipeptydil-peptidase I light chain
C: dipeptydil-peptidase I heavy chain
hetero molecules

A: dipeptydil-peptidase I exclusion domain
B: dipeptydil-peptidase I light chain
C: dipeptydil-peptidase I heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,48132
Polymers158,30212
Non-polymers2,17920
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area48180 Å2
ΔGint-493 kcal/mol
Surface area50970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.154, 88.031, 114.609
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Detailstetramer molecule with tetrahaedral symmetry

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Components

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Dipeptydil-peptidase I ... , 3 types, 3 molecules ABC

#1: Protein dipeptydil-peptidase I exclusion domain / DPPI / cathepsin C / residual propart


Mass: 13500.163 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): INSECT CELL(Invitrogen) / Cell line (production host): high five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein dipeptydil-peptidase I light chain / DPPI / cathepsin C / beta chain


Mass: 18491.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): INSECT CELL(Invitrogen) / Cell line (production host): high five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein dipeptydil-peptidase I heavy chain / DPPI / cathepsin C / alpha chain


Mass: 7583.444 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): INSECT CELL(Invitrogen) / Cell line (production host): high five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 468 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir
30.1 Msodium citrate1reservoir
40.2 Mpotassium/sodium tartrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. all: 23553 / Num. obs: 23553 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.15→2.18 Å / Num. unique all: 23353 / Rsym value: 0.249 / % possible all: 0.99
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 96833 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 99 % / Rmerge(I) obs: 0.249

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
SHARPphasing
MAINrefinement
RefinementMethod to determine structure: MAD, MIR, MOL. REPL together / Resolution: 2.15→10 Å / Isotropic thermal model: isotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1168 -each 20th measured reflection
Rwork0.19 ---
all0.186 23553 --
obs0.186 23353 5 %-
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 30 464 3278
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_deg1.54
X-RAY DIFFRACTIONo_bond_d0.009
Refinement
*PLUS
Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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