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- PDB-1g0v: THE STRUCTURE OF PROTEINASE A COMPLEXED WITH A IA3 MUTANT, MVV -

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Basic information

Entry
Database: PDB / ID: 1g0v
TitleTHE STRUCTURE OF PROTEINASE A COMPLEXED WITH A IA3 MUTANT, MVV
Components
  • PROTEASE A INHIBITOR 3
  • PROTEINASE A
Keywordshydrolase/hydrolase inhibitor / Proteinase A / MVV / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


saccharopepsin / protein catabolic process in the vacuole / : / microautophagy / oligosaccharide binding / cytoplasm to vacuole targeting by the Cvt pathway / pexophagy / fungal-type vacuole / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity ...saccharopepsin / protein catabolic process in the vacuole / : / microautophagy / oligosaccharide binding / cytoplasm to vacuole targeting by the Cvt pathway / pexophagy / fungal-type vacuole / negative regulation of endopeptidase activity / aspartic-type endopeptidase inhibitor activity / vacuole / endopeptidase inhibitor activity / Neutrophil degranulation / 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
alpha-D-mannopyranose / Protease A inhibitor 3 / Saccharopepsin
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsPhylip, L.H. / Lees, W. / Brownsey, B.G. / Bur, D. / Dunn, B.M. / Winther, J. / Gustchina, A. / Li, M. / Copeland, T. / Wlodawer, A. / Kay, J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The potency and specificity of the interaction between the IA3 inhibitor and its target aspartic proteinase from Saccharomyces cerevisiae.
Authors: Phylip, L.H. / Lees, W.E. / Brownsey, B.G. / Bur, D. / Dunn, B.M. / Winther, J.R. / Gustchina, A. / Li, M. / Copeland, T. / Wlodawer, A. / Kay, J.
#1: Journal: Nat.Struct.Biol. / Year: 2000
Title: The aspartic proteinase from Saccharomyces cerevisiae folds its own inhibitor into helix
Authors: Li, M. / Phylip, L.H. / Lees, W. / Winther, J. / Dunn, B. / Wlodawer, A. / Kay, J. / Gustchina, A.
History
DepositionOct 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: 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 / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_ref_seq_dif / 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 / _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_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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Advisory / Database references / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEINASE A
B: PROTEASE A INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9685
Polymers39,1692
Non-polymers1,7993
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint15 kcal/mol
Surface area14320 Å2
MethodPISA
2
A: PROTEINASE A
B: PROTEASE A INHIBITOR 3
hetero molecules

A: PROTEINASE A
B: PROTEASE A INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,93610
Polymers78,3394
Non-polymers3,5976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+11
Buried area12370 Å2
ΔGint37 kcal/mol
Surface area28150 Å2
MethodPISA
3
A: PROTEINASE A
B: PROTEASE A INHIBITOR 3
hetero molecules

A: PROTEINASE A
B: PROTEASE A INHIBITOR 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,93610
Polymers78,3394
Non-polymers3,5976
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area14280 Å2
ΔGint18 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.140, 191.140, 52.334
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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Protein / Protein/peptide / Non-polymers , 3 types, 231 molecules AB

#1: Protein PROTEINASE A / E.C.3.4.23.25 / SACCHAROPEPSIN PRECURSOR / ASPARTATE PROTEASE / PROTEINASE YSCA


Mass: 35675.422 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: P07267, saccharopepsin
#2: Protein/peptide PROTEASE A INHIBITOR 3 / CYTOPLASMIC INHIBITOR OF PROTEINASE PEP4P


Mass: 3493.913 Da / Num. of mol.: 1 / Fragment: MVV, A MUTANT OF IA3 / Mutation: K24M / Source method: obtained synthetically / References: UniProt: P01094
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 3 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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpa1-2[DManpa1-2DManpa1-6]DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-2-3-3/a4-b1_b4-c1_c3-d1_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]{}}}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#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 / N-Acetylglucosamine


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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 1500, (NH4)2SO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
230 %PEG15001reservoir
30.14 Mammonium sulfate1reservoir
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 41718 / Num. obs: 41718 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 7.3 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.346 / Num. unique all: 3327 / % possible all: 75.5
Reflection
*PLUS
Num. measured all: 217446
Reflection shell
*PLUS
% possible obs: 75.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementResolution: 2→24.41 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5393506.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1831 5 %RANDOM
Rwork0.198 ---
obs0.198 36484 94.8 %-
all-41718 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.59 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å2-0.77 Å20 Å2
2---2.64 Å20 Å2
3---5.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→24.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2743 0 120 229 3092
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 305 5.2 %
Rwork0.234 5614 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRA
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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