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- PDB-1nb5: Crystal structure of stefin A in complex with cathepsin H -

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Basic information

Entry
Database: PDB / ID: 1nb5
TitleCrystal structure of stefin A in complex with cathepsin H
Components
  • Cathepsin H
  • Cathepsin H MINI CHAIN
  • STEFIN A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEINASE / AMINOPEPTIDASE / CYSTATIN / ENZYME-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


cathepsin H / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / Surfactant metabolism / alveolar lamellar body / peptidase inhibitor complex / thyroid hormone binding / immune response-regulating signaling pathway / membrane protein proteolysis ...cathepsin H / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / Surfactant metabolism / alveolar lamellar body / peptidase inhibitor complex / thyroid hormone binding / immune response-regulating signaling pathway / membrane protein proteolysis / lysosomal protein catabolic process / peptide cross-linking / Formation of the cornified envelope / cornified envelope / bradykinin catabolic process / Neutrophil degranulation / metanephros development / surfactant homeostasis / cellular response to thyroid hormone stimulus / zymogen activation / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of epithelial cell migration / cysteine-type endopeptidase inhibitor activity / response to retinoic acid / aminopeptidase activity / keratinocyte differentiation / ERK1 and ERK2 cascade / negative regulation of proteolysis / cysteine-type peptidase activity / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / cell-cell adhesion / T cell mediated cytotoxicity / protein destabilization / cytoplasmic ribonucleoprotein granule / protease binding / endopeptidase activity / lysosome / immune response / positive regulation of cell migration / serine-type endopeptidase activity / cysteine-type endopeptidase activity / positive regulation of gene expression / proteolysis / extracellular space / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) ...Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / 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 / Nuclear Transport Factor 2; Chain: A, / Papain-like cysteine peptidase superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Pro-cathepsin H / Cystatin-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJenko, S. / Dolenc, I. / Guncar, G. / Dobersek, A. / Podobnik, M. / Turk, D.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo- and exopeptidases
Authors: Jenko, S. / Dolenc, I. / Guncar, G. / Dobersek, A. / Podobnik, M. / Turk, D.
History
DepositionDec 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / 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 / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / 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 / pdbx_unobs_or_zero_occ_residues / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Revision 2.2Oct 16, 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: Cathepsin H
P: Cathepsin H MINI CHAIN
I: STEFIN A
B: Cathepsin H
R: Cathepsin H MINI CHAIN
J: STEFIN A
C: Cathepsin H
S: Cathepsin H MINI CHAIN
K: STEFIN A
D: Cathepsin H
T: Cathepsin H MINI CHAIN
L: STEFIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,13816
Polymers144,79112
Non-polymers2,3464
Water00
1
A: Cathepsin H
P: Cathepsin H MINI CHAIN
I: STEFIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7844
Polymers36,1983
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-6 kcal/mol
Surface area14090 Å2
MethodPISA
2
B: Cathepsin H
R: Cathepsin H MINI CHAIN
J: STEFIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7844
Polymers36,1983
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-4 kcal/mol
Surface area14040 Å2
MethodPISA
3
C: Cathepsin H
S: Cathepsin H MINI CHAIN
K: STEFIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7844
Polymers36,1983
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-7 kcal/mol
Surface area14030 Å2
MethodPISA
4
D: Cathepsin H
T: Cathepsin H MINI CHAIN
L: STEFIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7844
Polymers36,1983
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-6 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.629, 97.575, 162.188
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
Cathepsin H


Mass: 24328.521 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: spleen / Source: (natural) Sus scrofa (pig) / References: UniProt: O46427, cathepsin H
#2: Protein/peptide
Cathepsin H MINI CHAIN


Mass: 848.878 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: spleen / Source: (natural) Sus scrofa (pig) / References: UniProt: O46427, cathepsin H
#3: Protein
STEFIN A / Cystatin AS / Cystatin A


Mass: 11020.464 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTA OR STF1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01040
#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
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: 2.51 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: PEG 4000, ammonium sulphate, sodium acetate, cadmium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
118 %(w/v)PEG40001reservoir
20.18 Mammonium sulfate1reservoir
30.1 Msodium acetate1reservoirpH4.2
47 mg/mlprotein1drop
540 mM1dropCdCl2

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2001 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.4→38.03 Å / Num. obs: 56687 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.9 % / Rsym value: 0.104
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6750 / Rsym value: 0.342 / % possible all: 96.8
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 99 Å / Num. obs: 56687 / % possible obs: 98.4 % / Num. measured all: 1185453 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 96.8 % / Rmerge(I) obs: 0.342

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MAINrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1STF, 8PCH

1stf

8pch


Resolution: 2.4→10 Å / Isotropic thermal model: Isotropic / Cross valid method: R-FREE,KICKED OMIT MAP / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.274 2837 10 %
Rwork0.235 --
all0.235 56733 -
obs-55861 -
Displacement parametersBiso mean: 40.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10156 0 156 0 10312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.013
X-RAY DIFFRACTIONo_angle_deg1.87
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 41462
Solvent computation
*PLUS
Displacement parameters
*PLUS

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