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- PDB-3qz2: The structure of cysteine-free human insulin degrading enzyme -

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Basic information

Entry
Database: PDB / ID: 3qz2
TitleThe structure of cysteine-free human insulin degrading enzyme
ComponentsInsulin-degrading enzyme
KeywordsHYDROLASE / insulin degrading enzyme
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 / metalloendopeptidase activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / peroxisome / positive regulation of protein catabolic process / virus receptor activity / insulin receptor signaling pathway / positive regulation of protein binding / basolateral plasma membrane / endopeptidase activity / Ub-specific processing proteases / external side of plasma membrane / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
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
Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGuo, Q. / Tang, W.J.
CitationJournal: Eur.J.Med.Chem. / Year: 2014
Title: Imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-beta hydrolysis.
Authors: Charton, J. / Gauriot, M. / Guo, Q. / Hennuyer, N. / Marechal, X. / Dumont, J. / Hamdane, M. / Pottiez, V. / Landry, V. / Sperandio, O. / Flipo, M. / Buee, L. / Staels, B. / Leroux, F. / ...Authors: Charton, J. / Gauriot, M. / Guo, Q. / Hennuyer, N. / Marechal, X. / Dumont, J. / Hamdane, M. / Pottiez, V. / Landry, V. / Sperandio, O. / Flipo, M. / Buee, L. / Staels, B. / Leroux, F. / Tang, W.J. / Deprez, B. / Deprez-Poulain, R.
History
DepositionMar 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 28, 2014Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,2544
Polymers229,1232
Non-polymers1312
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)262.073, 262.073, 90.838
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 114561.562 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14735, insulysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10-13% PEG MME 5000, 100 mM HEPES pH 7.0, 4-14% Tacsimate, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9597 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 19, 2010
RadiationMonochromator: MAR CCD / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9597 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 55731 / Num. obs: 55620 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→50 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.864 / SU B: 16.537 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24072 2967 5.1 %RANDOM
Rwork0.17166 ---
obs0.17514 55620 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15570 0 2 176 15748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02215944
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.96721564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.88551898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16524.52792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.332152860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7661582
X-RAY DIFFRACTIONr_chiral_restr0.1170.22323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112142
X-RAY DIFFRACTIONr_mcbond_it0.6111.59534
X-RAY DIFFRACTIONr_mcangle_it1.266215428
X-RAY DIFFRACTIONr_scbond_it1.99636410
X-RAY DIFFRACTIONr_scangle_it3.5864.56136
LS refinement shellResolution: 3.205→3.288 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 220 -
Rwork0.228 4042 -
obs--98.59 %

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