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Basic information

Entry
Database: PDB / ID: 5uoe
TitleCrystal Structure Analysis of Elbow-Engineered-Fab-Bound Human Insulin Degrading Enzyme (IDE)
Components
  • FAB Heavy chain with engineered elbow
  • FAB light chain
  • Insulin-degrading enzyme
KeywordsHydrolase/Immune System / Hydrolase / FAB / elbow-engineer / Hydrolase-Immune System complex
Function / homology
Function and homology information


insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / cytosolic proteasome complex / insulin binding ...insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / cytosolic proteasome complex / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / positive regulation of protein binding / Insulin receptor recycling / negative regulation of proteolysis / peptide binding / proteolysis involved in protein catabolic process / Peroxisomal protein import / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / insulin receptor signaling pathway / peroxisome / amyloid-beta binding / virus receptor activity / endopeptidase activity / basolateral plasma membrane / Ub-specific processing proteases / external side of plasma membrane / protein-containing complex binding / cell surface / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / 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, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsLiang, W.G. / Bailey, L. / Kossiakoff, T. / Tang, W.J.
CitationJournal: To Be Published
Title: Crystal Structure Analysis of Elbow-Engineered-Fab-Bound Human Insulin Degrading Enzyme (IDE)
Authors: Liang, W.G. / Bailey, L. / Kossiakoff, T. / Tang, W.J.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: Insulin-degrading enzyme
D: Insulin-degrading enzyme
E: Insulin-degrading enzyme
H: FAB Heavy chain with engineered elbow
L: FAB light chain
M: FAB Heavy chain with engineered elbow
N: FAB light chain
P: FAB Heavy chain with engineered elbow
Q: FAB light chain
S: FAB Heavy chain with engineered elbow
T: FAB light chain
V: FAB Heavy chain with engineered elbow
W: FAB light chain


Theoretical massNumber of molelcules
Total (without water)811,09315
Polymers811,09315
Non-polymers00
Water00
1
A: Insulin-degrading enzyme
H: FAB Heavy chain with engineered elbow
L: FAB light chain


Theoretical massNumber of molelcules
Total (without water)162,2193
Polymers162,2193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-21 kcal/mol
Surface area47160 Å2
MethodPISA
2
B: Insulin-degrading enzyme
M: FAB Heavy chain with engineered elbow
N: FAB light chain


Theoretical massNumber of molelcules
Total (without water)162,2193
Polymers162,2193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-23 kcal/mol
Surface area47230 Å2
MethodPISA
3
C: Insulin-degrading enzyme
P: FAB Heavy chain with engineered elbow
Q: FAB light chain


Theoretical massNumber of molelcules
Total (without water)162,2193
Polymers162,2193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-23 kcal/mol
Surface area46540 Å2
MethodPISA
4
D: Insulin-degrading enzyme
S: FAB Heavy chain with engineered elbow
T: FAB light chain


Theoretical massNumber of molelcules
Total (without water)162,2193
Polymers162,2193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-22 kcal/mol
Surface area46710 Å2
MethodPISA
5
E: Insulin-degrading enzyme
V: FAB Heavy chain with engineered elbow
W: FAB light chain


Theoretical massNumber of molelcules
Total (without water)162,2193
Polymers162,2193
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-22 kcal/mol
Surface area46690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.321, 242.048, 310.757
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 114561.562 Da / Num. of mol.: 5
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 / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin
#2: Antibody
FAB Heavy chain with engineered elbow


Mass: 24251.062 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody
FAB light chain


Mass: 23405.961 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.088M Ammonium citrate tribasic, ph 7, 10% w/v peg3350, 0.02 M Ethylenediaminetetraacetic disodium salt dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 97999 / % possible obs: 100 % / Observed criterion σ(I): 2.65 / Redundancy: 6.6 % / Net I/σ(I): 7.95
Reflection shellResolution: 3.8→3.87 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.65 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IOF

4iof


Resolution: 3.8→49.237 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 1986 2.03 %
Rwork0.2201 --
obs0.2211 97998 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→49.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47331 0 0 0 47331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00348514
X-RAY DIFFRACTIONf_angle_d0.59365699
X-RAY DIFFRACTIONf_dihedral_angle_d7.57729177
X-RAY DIFFRACTIONf_chiral_restr0.0427117
X-RAY DIFFRACTIONf_plane_restr0.0048474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8-3.8950.33681400.26626767X-RAY DIFFRACTION100
3.895-4.00030.30691400.24986786X-RAY DIFFRACTION100
4.0003-4.11790.26911420.22616830X-RAY DIFFRACTION100
4.1179-4.25080.2521410.22156784X-RAY DIFFRACTION100
4.2508-4.40260.28281410.20926798X-RAY DIFFRACTION100
4.4026-4.57870.27331400.1986787X-RAY DIFFRACTION100
4.5787-4.7870.21381400.19436810X-RAY DIFFRACTION100
4.787-5.03910.25261440.2026863X-RAY DIFFRACTION100
5.0391-5.35450.31571400.21626811X-RAY DIFFRACTION100
5.3545-5.76730.27311420.21946885X-RAY DIFFRACTION100
5.7673-6.34660.29081430.23576875X-RAY DIFFRACTION100
6.3466-7.26250.27151430.23276918X-RAY DIFFRACTION100
7.2625-9.14040.2381450.20296982X-RAY DIFFRACTION100
9.1404-49.24090.26171450.237116X-RAY DIFFRACTION98

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