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- PDB-1nb3: Crystal structure of stefin A in complex with cathepsin H: N-term... -

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Basic information

Entry
Database: PDB / ID: 1nb3
TitleCrystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo-and exopeptidases
Components
  • CATHEPSIN H MINI CHAIN
  • Cathepsin H
  • Stefin ACystatin A
KeywordsHYDROLASE / CYSTEINE PROTEINASE / AMINOPEPTIDASE / CYSTATIN / ENZYME-INHIBITOR COMPLEX
Function / homology
Function and homology information


cathepsin H / immune response-regulating signaling pathway / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / Surfactant metabolism / positive regulation of peptidase activity / alveolar lamellar body / negative regulation of peptidase activity / peptidase inhibitor complex ...cathepsin H / immune response-regulating signaling pathway / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / Surfactant metabolism / positive regulation of peptidase activity / alveolar lamellar body / negative regulation of peptidase activity / peptidase inhibitor complex / membrane protein proteolysis / Formation of the cornified envelope / peptide cross-linking / Neutrophil degranulation / bradykinin catabolic process / cornified envelope / metanephros development / surfactant homeostasis / zymogen activation / MHC class II antigen presentation / cysteine-type endopeptidase inhibitor activity / positive regulation of epithelial cell migration / thyroid hormone binding / cysteine-type endopeptidase activator activity involved in apoptotic process / aminopeptidase activity / response to retinoic acid / keratinocyte differentiation / cysteine-type peptidase activity / ERK1 and ERK2 cascade / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / negative regulation of proteolysis / protein destabilization / T cell mediated cytotoxicity / cell-cell adhesion / positive regulation of angiogenesis / endopeptidase activity / protease binding / lysosome / positive regulation of cell migration / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / proteolysis / extracellular space / nucleoplasm / cytosol / cytoplasm
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.type
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_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

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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
Water9,782543
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-8 kcal/mol
Surface area14160 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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-6 kcal/mol
Surface area14280 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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-6 kcal/mol
Surface area14270 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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-7 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.584, 91.630, 161.235
Angle α, β, γ (deg.)90.00, 93.69, 90.00
Int Tables number4
Space group name H-MP1211

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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: protein was isolated from 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: protein was isolated from spleen / Source: (natural) Sus scrofa (pig) / References: UniProt: O46427, cathepsin H
#3: Protein
Stefin A / Cystatin 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.36 Å3/Da / Density % sol: 47.39 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 4.2 / 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 2001 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. obs: 34127 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Rsym value: 0.161
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 4.7 / Num. unique all: 3405 / Rsym value: 0.583 / % possible all: 97.4
Reflection
*PLUS
Lowest resolution: 99 Å / Num. obs: 35154 / % possible obs: 97.4 % / Num. measured all: 313477 / Rmerge(I) obs: 0.161
Reflection shell
*PLUS
% possible obs: 97.1 % / Rmerge(I) obs: 0.583

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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: 2.8→10 Å / Cross valid method: R-FREE, KICKED OMIT MAP / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.246 1637 10 %
Rwork0.2265 --
all0.228 34572 -
obs-32744 -
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10156 0 156 543 10855
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.012
X-RAY DIFFRACTIONo_angle_deg1.74
LS refinement shellHighest resolution: 2.8 Å
RfactorNum. reflection
Rfree0.246 1637
Rwork0.228 -
obs-34572
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.8 Å

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