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- PDB-4iof: Crystal structure analysis of Fab-bound human Insulin Degrading E... -

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Basic information

Entry
Database: PDB / ID: 4iof
TitleCrystal structure analysis of Fab-bound human Insulin Degrading Enzyme (IDE)
Components
  • Fab-bound IDE, heavy chain
  • Fab-bound IDE, light chain
  • Insulin-degrading enzyme
KeywordsHYDROLASE / Zinc metalloprotease
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.353 Å
AuthorsMcCord, L.A. / Liang, W.G. / Hoey, R. / Dowdell, E. / Koide, A. / Koide, S. / Tang, W.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Conformational states and recognition of amyloidogenic peptides of human insulin-degrading enzyme.
Authors: McCord, L.A. / Liang, W.G. / Dowdell, E. / Kalas, V. / Hoey, R.J. / Koide, A. / Koide, S. / Tang, W.J.
History
DepositionJan 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Sep 4, 2013Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

Downloads & links

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Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
C: Fab-bound IDE, heavy chain
D: Fab-bound IDE, light chain
E: Fab-bound IDE, heavy chain
F: Fab-bound IDE, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,5567
Polymers337,4916
Non-polymers651
Water181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.955, 131.662, 377.039
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDE, Insulin Degrading Enzyme / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin
#2: Antibody Fab-bound IDE, heavy chain


Mass: 28201.670 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Antibody Fab-bound IDE, light chain


Mass: 25982.098 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Sodium cacodylate, pH6.5; 0.2M MgCl2; 10% PEG3000, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.353→50 Å / Num. all: 41849 / Num. obs: 40227 / % possible obs: 99.9 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 3.2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.119 / Rsym value: 0.119 / Net I/σ(I): 14.1
Reflection shellResolution: 3.353→3.42 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.688 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CWW

3cww


Resolution: 3.353→49.852 Å / SU ML: 0.43 / Phase error: 26.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2803 2010 5 %Random
Rwork0.2322 ---
all0.2346 41849 --
obs0.2346 40227 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.353→49.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20937 0 1 1 20939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621433
X-RAY DIFFRACTIONf_angle_d1.57828986
X-RAY DIFFRACTIONf_dihedral_angle_d16.7317939
X-RAY DIFFRACTIONf_chiral_restr0.1053187
X-RAY DIFFRACTIONf_plane_restr0.0083693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.353-3.43680.29391020.25251904X-RAY DIFFRACTION36
3.4368-3.52970.31611160.25852309X-RAY DIFFRACTION43
3.5297-3.63360.31441390.26082614X-RAY DIFFRACTION49
3.6336-3.75080.30171470.24052753X-RAY DIFFRACTION52
3.7508-3.88480.27591480.24582811X-RAY DIFFRACTION53
3.8848-4.04030.29541490.24452821X-RAY DIFFRACTION53
4.0403-4.22410.30261470.23762798X-RAY DIFFRACTION53
4.2241-4.44670.24641480.22112821X-RAY DIFFRACTION53
4.4467-4.72510.27771510.21172856X-RAY DIFFRACTION53
4.7251-5.08950.27311490.20332822X-RAY DIFFRACTION53
5.0895-5.60110.27451500.23172862X-RAY DIFFRACTION54
5.6011-6.41020.29181510.24852883X-RAY DIFFRACTION54
6.4102-8.07060.29251540.24192924X-RAY DIFFRACTION55
8.0706-49.85780.24451590.21243039X-RAY DIFFRACTION57

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