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- PDB-2djg: Re-determination of the native structure of human dipeptidyl pept... -

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Basic information

Entry
Database: PDB / ID: 2djg
TitleRe-determination of the native structure of human dipeptidyl peptidase I (cathepsin C)
Components(Dipeptidyl-peptidase ...) x 3
KeywordsHYDROLASE / re-refinement / cysteine protease / cathepsin C / dipeptidyl peptidase I
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMolgaard, A. / Arnau, J. / Lauritzen, C. / Larsen, S. / Petersen, G. / Pedersen, J.
CitationJournal: Biochem.J. / Year: 2007
Title: The crystal structure of human dipeptidyl peptidase I (cathepsin C) in complex with the inhibitor Gly-Phe-CHN2
Authors: Molgaard, A. / Arnau, J. / Lauritzen, C. / Larsen, S. / Petersen, G. / Pedersen, J.
History
DepositionApr 2, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1569
Polymers39,5753
Non-polymers1,5816
Water3,801211
1
A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules

A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules

A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules

A: Dipeptidyl-peptidase 1
B: Dipeptidyl-peptidase 1
C: Dipeptidyl-peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,62536
Polymers158,30212
Non-polymers6,32324
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 area51210 Å2
ΔGint-357 kcal/mol
Surface area52620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.479, 88.680, 114.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Dipeptidyl-peptidase ... , 3 types, 3 molecules ABC

#1: Protein Dipeptidyl-peptidase 1 / Cathepsin C


Mass: 13500.163 Da / Num. of mol.: 1 / Fragment: Dipeptidyl-peptidase 1 exclusion domain chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC / Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#2: Protein Dipeptidyl-peptidase 1 / Cathepsin C


Mass: 18491.871 Da / Num. of mol.: 1 / Fragment: Dipeptidyl-peptidase 1 heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC / Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I
#3: Protein Dipeptidyl-peptidase 1 / Cathepsin C


Mass: 7583.444 Da / Num. of mol.: 1 / Fragment: Dipeptidyl-peptidase 1 light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC / Cell (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I

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Sugars , 2 types, 3 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE
#5: 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.: 2
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, 214 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.8 Å3/Da / Density % sol: 56.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.8M ammonium sulfate, 0.1M Na citrate, 0.2M Na/K tartrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 120690 / Num. obs: 120690
Reflection shellResolution: 2.05→2.12 Å / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1k3b

1k3b


Resolution: 2.05→24.04 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.62 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22076 1376 5.1 %RANDOM
Rwork0.17375 ---
all0.17612 25787 --
obs0.17612 25787 96.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.055 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.05→24.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2720 0 100 211 3031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212907
X-RAY DIFFRACTIONr_bond_other_d0.0020.022436
X-RAY DIFFRACTIONr_angle_refined_deg1.8491.9643957
X-RAY DIFFRACTIONr_angle_other_deg0.97835654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8725339
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1370.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023171
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02618
X-RAY DIFFRACTIONr_nbd_refined0.2390.2556
X-RAY DIFFRACTIONr_nbd_other0.2560.22834
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.090.21550
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2176
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1151.51693
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99322716
X-RAY DIFFRACTIONr_scbond_it2.6631214
X-RAY DIFFRACTIONr_scangle_it4.0664.51241
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 101
Rwork0.231 1862

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