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- PDB-1dpj: THE STRUCTURE OF PROTEINASE A COMPLEXED WITH IA3 PEPTIDE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1dpj
TitleTHE STRUCTURE OF PROTEINASE A COMPLEXED WITH IA3 PEPTIDE INHIBITOR
Components
  • PROTEINASE A
  • PROTEINASE INHIBITOR IA3 PEPTIDE
KeywordsHYDROLASE/HYDROLASE INHIBITOR / proteinase A / IA3 peptide / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


saccharopepsin / protein catabolic process in the vacuole / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / fungal-type vacuole / vacuole ...saccharopepsin / protein catabolic process in the vacuole / microautophagy / cytoplasm to vacuole targeting by the Cvt pathway / oligosaccharide binding / pexophagy / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / fungal-type vacuole / vacuole / endopeptidase inhibitor activity / proteolysis involved in protein catabolic process / macroautophagy / autophagy / disordered domain specific binding / peptidase activity / protease binding / aspartic-type endopeptidase activity / endoplasmic reticulum / protein-containing complex / mitochondrion / nucleus / cytoplasm
Similarity search - Function
Protease A inhibitor IA3 domain superfamily / Protease A inhibitor IA3 / Saccharopepsin inhibitor I34 / Saccharopepsin / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases ...Protease A inhibitor IA3 domain superfamily / Protease A inhibitor IA3 / Saccharopepsin inhibitor I34 / Saccharopepsin / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Protease A inhibitor 3 / Saccharopepsin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsLi, M. / Phylip, H.L. / Lees, W.E. / Winther, J.R. / Dunn, B.M. / Wlodawer, A. / Kay, J. / Guschina, A.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into a helix.
Authors: Li, M. / Phylip, L.H. / Lees, W.E. / Winther, J.R. / Dunn, B.M. / Wlodawer, A. / Kay, J. / Gustchina, A.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: The Three-dimensional Structure at 2.4 A Resolution of Glycosylated Proteinase A from the Lysosome-like Vacuole of Saccharomyces Cerevisiae
Authors: Aguilar, C.F. / Cronin, N.B. / Badasso, M. / Dreyer, T. / Newman, M.P. / Cooper, J.B. / Hoover, D.J. / Wood, S.P. / Johnson, M.S. / Blundell, T.L.
History
DepositionDec 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: 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_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jul 7, 2021Group: Refinement description / Structure summary / Category: chem_comp / refine
Item: _chem_comp.pdbx_synonyms / _refine.ls_percent_reflns_obs

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6328
Polymers39,4672
Non-polymers2,1656
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-30 kcal/mol
Surface area14410 Å2
MethodPISA
2
A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3 PEPTIDE
hetero molecules

A: PROTEINASE A
B: PROTEINASE INHIBITOR IA3 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,26316
Polymers78,9334
Non-polymers4,33012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area15800 Å2
ΔGint-89 kcal/mol
Surface area26270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.660, 191.660, 52.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11B-804-

SO4

21A-1147-

HOH

31A-1148-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein PROTEINASE A / ASPARTATE PROTEASE


Mass: 35774.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07267, saccharopepsin
#2: Protein/peptide PROTEINASE INHIBITOR IA3 PEPTIDE / IA3


Mass: 3692.155 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P01094

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpa1-2[DManpa1-2DManpa1-6]DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-i1_d2-e1_d6-g1_e2-f1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][b-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#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 , 2 types, 376 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE RESIDUE NUMBERS FOR CHAIN A FOLLOW THE RESIDUE NUMBERS IN PDB ENTRY 2JXR. THE SEQUENCE FOR ...THE RESIDUE NUMBERS FOR CHAIN A FOLLOW THE RESIDUE NUMBERS IN PDB ENTRY 2JXR. THE SEQUENCE FOR CHAIN B IS TRUNCATED.

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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: 3.5 Å3/Da / Density % sol: 64.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 1500, Ammounia Sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
228 %PEG15001reservoir
30.2 Mammonium sulfate1reservoir
40.1 MMES1reservoir
520 mMMES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. all: 53659 / Num. obs: 53659 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 24
Reflection shellResolution: 1.78→1.84 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.71 / Num. unique all: 5236 / % possible all: 98.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 99.1 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 1.8→30 Å / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2437 -random
Rwork0.192 ---
all-48773 --
obs-48773 99 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2742 0 139 372 3253
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.8
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / σ(F): 0 / Rfactor obs: 0.2055
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.8

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