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- PDB-3hgz: Crystal structure of human insulin-degrading enzyme in complex wi... -

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Basic information

Entry
Database: PDB / ID: 3hgz
TitleCrystal structure of human insulin-degrading enzyme in complex with amylin
Components
  • Insulin-degrading enzyme
  • Islet amyloid polypeptide
KeywordsHYDROLASE / Insulin degrading enzyme / IDE / Amylin / cystein free / Cytoplasm / Metal-binding / Metalloprotease / Polymorphism / Protease / Zinc / Amidation / Amyloid / Cleavage on pair of basic residues / Disulfide bond / Hormone / Secreted
Function / homology
Function and homology information


insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amyloid-beta clearance by cellular catabolic process / amylin receptor 1 signaling pathway / amylin receptor signaling pathway ...insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amyloid-beta clearance by cellular catabolic process / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / Calcitonin-like ligand receptors / hormone catabolic process / bradykinin catabolic process / cytosolic proteasome complex / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / insulin binding / regulation of aerobic respiration / peptide catabolic process / negative regulation of osteoclast differentiation / amyloid-beta clearance / Regulation of gene expression in beta cells / positive regulation of cAMP/PKA signal transduction / peroxisomal matrix / amyloid-beta metabolic process / bone resorption / negative regulation of protein-containing complex assembly / Insulin receptor recycling / negative regulation of proteolysis / sensory perception of pain / peptide binding / positive regulation of calcium-mediated signaling / proteolysis involved in protein catabolic process / osteoclast differentiation / Peroxisomal protein import / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / hormone activity / metalloendopeptidase activity / positive regulation of protein binding / positive regulation of protein catabolic process / peroxisome / insulin receptor signaling pathway / cell-cell signaling / amyloid-beta binding / virus receptor activity / G alpha (s) signalling events / basolateral plasma membrane / endopeptidase activity / positive regulation of MAPK cascade / Ub-specific processing proteases / positive regulation of apoptotic process / receptor ligand activity / Amyloid fiber formation / external side of plasma membrane / signaling receptor binding / neuronal cell body / apoptotic process / lipid binding / protein-containing complex binding / cell surface / signal transduction / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / extracellular region / 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 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / Islet amyloid polypeptide / Calcitonin-like / Calcitonin peptide-like / Calcitonin, conserved site / Calcitonin / CGRP / IAPP family signature. / calcitonin / Calcitonin/adrenomedullin / Calcitonin / CGRP / IAPP family / 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
Islet amyloid polypeptide / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsGuo, Q. / Bian, Y. / Tang, W.J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular Basis for the Recognition and Cleavages of IGF-II, TGF-alpha, and Amylin by Human Insulin-Degrading Enzyme.
Authors: Guo, Q. / Manolopoulou, M. / Bian, Y. / Schilling, A.B. / Tang, W.J.
History
DepositionMay 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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.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
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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
D: Islet amyloid polypeptide
E: Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,2896
Polymers232,1584
Non-polymers1312
Water6,251347
1
A: Insulin-degrading enzyme
D: Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1443
Polymers116,0792
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-44 kcal/mol
Surface area38520 Å2
MethodPISA
2
B: Insulin-degrading enzyme
E: Islet amyloid polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,1443
Polymers116,0792
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-49 kcal/mol
Surface area38730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.868, 262.868, 90.854
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 / Insulin protease / Insulinase / Insulysin


Mass: 112169.727 Da / Num. of mol.: 2
Mutation: C110L, E111Q, 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-CF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(de3) / References: UniProt: P14735, insulysin
#2: Protein/peptide Islet amyloid polypeptide / Amylin / Diabetes-associated peptide / DAP / Insulinoma amyloid peptide


Mass: 3909.304 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: UniProt: P10997
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97323 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97323 Å / Relative weight: 1
ReflectionResolution: 2.91→50 Å / Num. all: 79043 / Num. obs: 79043 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.91→2.982 Å / Rmerge(I) obs: 0.332 / Num. unique all: 7788 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.91→49.69 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.422 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.648 / ESU R Free: 0.307 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22388 3963 5 %RANDOM
Rwork0.17579 ---
obs0.1782 75049 99.85 %-
all-79045 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.643 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.91→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15807 0 2 347 16156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02216199
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.96721909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98451925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12324.566806
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.942152908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8771582
X-RAY DIFFRACTIONr_chiral_restr0.0960.22357
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212344
X-RAY DIFFRACTIONr_nbd_refined0.2410.28092
X-RAY DIFFRACTIONr_nbtor_refined0.3180.211127
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2657
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.211
X-RAY DIFFRACTIONr_mcbond_it0.6031.59838
X-RAY DIFFRACTIONr_mcangle_it1.054215670
X-RAY DIFFRACTIONr_scbond_it1.60737034
X-RAY DIFFRACTIONr_scangle_it2.8324.56239
LS refinement shellResolution: 2.91→2.982 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 292 -
Rwork0.27 5384 -
obs--98.1 %

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