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- PDB-3e4a: Human IDE-inhibitor complex at 2.6 angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 3e4a
TitleHuman IDE-inhibitor complex at 2.6 angstrom resolution
Components
  • HYDROXAMATE PEPTIDE II1
  • Insulin-degrading enzyme
KeywordsHYDROLASE / INSULIN / HYDROXAMATE / INSULIN DEGRADING ENZYME / Metal-binding / Metalloprotease / Protease
Function / homology
Function and homology information


insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / regulation of aerobic respiration ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / ubiquitin-modified protein reader activity / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / proteolysis involved in protein catabolic process / Peroxisomal protein import / peptide binding / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / peroxisome / positive regulation of protein binding / insulin receptor signaling pathway / virus receptor activity / basolateral plasma membrane / endopeptidase activity / Ub-specific processing proteases / external side of plasma membrane / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / zinc ion binding / extracellular exosome / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / 1,4-DIETHYLENE DIOXIDE / Chem-QIX / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMalito, E. / Leissring, M.A. / Choi, S. / Cuny, G.D. / Tang, W.J.
CitationJournal: Plos One / Year: 2010
Title: Designed inhibitors of insulin-degrading enzyme regulate the catabolism and activity of insulin.
Authors: Leissring, M.A. / Malito, E. / Hedouin, S. / Reinstatler, L. / Sahara, T. / Abdul-Hay, S.O. / Choudhry, S. / Maharvi, G.M. / Fauq, A.H. / Huzarska, M. / May, P.S. / Choi, S. / Logan, T.P. / ...Authors: Leissring, M.A. / Malito, E. / Hedouin, S. / Reinstatler, L. / Sahara, T. / Abdul-Hay, S.O. / Choudhry, S. / Maharvi, G.M. / Fauq, A.H. / Huzarska, M. / May, P.S. / Choi, S. / Logan, T.P. / Turk, B.E. / Cantley, L.C. / Manolopoulou, M. / Tang, W.J. / Stein, R.L. / Cuny, G.D. / Selkoe, D.J.
History
DepositionAug 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: pdbx_entity_src_syn / software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
F: HYDROXAMATE PEPTIDE II1
G: HYDROXAMATE PEPTIDE II1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)239,07329
Polymers236,4004
Non-polymers2,67325
Water6,702372
1
A: Insulin-degrading enzyme
F: HYDROXAMATE PEPTIDE II1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,46514
Polymers118,2002
Non-polymers1,26512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-29.4 kcal/mol
Surface area37900 Å2
MethodPISA
2
B: Insulin-degrading enzyme
G: HYDROXAMATE PEPTIDE II1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,60915
Polymers118,2002
Non-polymers1,40913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-21.1 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.402, 261.402, 92.054
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABFG

#1: Protein Insulin-degrading enzyme / Insulysin / Insulinase / Insulin protease


Mass: 117968.664 Da / Num. of mol.: 2
Mutation: C110L, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDE / Plasmid: PPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA DE3 / References: UniProt: P14735, insulysin
#2: Protein/peptide HYDROXAMATE PEPTIDE II1


Mass: 231.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 397 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-QIX / N~2~-[(2R)-4-(HYDROXYAMINO)-2-(2-NAPHTHYLMETHYL)-4-OXOBUTANOYL]-L-ARGINYLGLYCYLGLYCINAMIDE


Mass: 542.587 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H34N8O6
#5: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H8O2
#6: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H4O2
#7: 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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 67.95 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG MME 5000, HEPES PH 7.0, TACSIMATE, DIOXANE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K, pH 7.00, temperature 291.5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2007
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 106959 / % possible obs: 97.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.094
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.437 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
SBC-Collectcollectdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JG4

2jg4


Resolution: 2.6→45.28 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5409 5.06 %RANDOM
Rwork0.167 ---
obs-106925 97.2 %-
Displacement parametersBiso mean: 38.03 Å2
Baniso -1Baniso -2Baniso -3
1--4.013 Å20 Å20 Å2
2---4.013 Å20 Å2
3---8.71 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15722 0 178 372 16272
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.3931
X-RAY DIFFRACTIONf_bond_deg0.0151
X-RAY DIFFRACTIONfHIRAL0.0951
X-RAY DIFFRACTIONf_dihedral_angle_d13.8511
X-RAY DIFFRACTIONfLANE0.0061
X-RAY DIFFRACTIONfonbonded4.0731

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