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- PDB-3n56: Crystal Structure of human Insulin-degrading enzyme (IDE) in comp... -

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Basic information

Entry
Database: PDB / ID: 3n56
TitleCrystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP)
Components
  • Insulin-degrading enzyme
  • Natriuretic peptides B
KeywordsHYDROLASE/HORMONE / INSULYSIN / INSULINASE / A-BETA DEGRADING ENZYME / CRYPTIDASE / HYDROLASE / HORMONE / DISEASE MUTATION / DIABETES MELLITUS / INSULIN / CARDIAC / SECRETED / PROTEASE / DISULFIDE BOND / METALLOPROTEASE / HUMAN INSULIN-DEGRADNG ENZYME / METAL-BINDING / NATRIURETIC PEPTIDE / NATRIURETIC FACTOR / CARDIOVASCULAR REGULATION / HYDROLASE-HORMONE complex
Function / homology
Function and homology information


diuretic hormone activity / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / insulysin / beta-endorphin binding / cGMP biosynthetic process / ubiquitin recycling / insulin catabolic process / insulin metabolic process ...diuretic hormone activity / body fluid secretion / receptor guanylyl cyclase signaling pathway / positive regulation of renal sodium excretion / insulysin / beta-endorphin binding / cGMP biosynthetic process / ubiquitin recycling / insulin catabolic process / insulin metabolic process / cardiac conduction system development / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / regulation of vascular permeability / positive regulation of urine volume / cytosolic proteasome complex / hormone receptor binding / negative regulation of systemic arterial blood pressure / : / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / neuropeptide signaling pathway / positive regulation of protein binding / Insulin receptor recycling / negative regulation of proteolysis / peptide binding / proteolysis involved in protein catabolic process / negative regulation of angiogenesis / blood vessel diameter maintenance / Peroxisomal protein import / protein catabolic process / negative regulation of cell growth / hormone activity / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / regulation of blood pressure / vasodilation / positive regulation of protein catabolic process / insulin receptor signaling pathway / peroxisome / protein folding / amyloid-beta binding / virus receptor activity / endopeptidase activity / basolateral plasma membrane / cell surface receptor signaling pathway / Ub-specific processing proteases / signaling receptor binding / external side of plasma membrane / protein-containing complex binding / cell surface / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Natriuretic peptide, brain type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : ...Natriuretic peptide, brain type / : / Natriuretic peptide, conserved site / Atrial natriuretic peptide / Natriuretic peptides signature. / Natriuretic peptide / Natriuretic peptide / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Insulin-degrading enzyme / Natriuretic peptides B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.102 Å
AuthorsFunke, T. / Guo, Q. / Tang, W.-J.
CitationJournal: To be Published
Title: Crystal Structure of human Insulin-degrading enzyme (IDE) in complex with human B-type natriuretic peptide (BNP)
Authors: Ralat, L.A. / Funke, T. / Ren, M. / Guo, Q. / Dickey, D.M. / Potter, L.R. / Tang, W.-J.
History
DepositionMay 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_seq_id / _struct_conn.ptnr2_label_asym_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: Natriuretic peptides B
D: Natriuretic peptides B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,3768
Polymers236,0694
Non-polymers3074
Water97354
1
A: Insulin-degrading enzyme
C: Natriuretic peptides B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1884
Polymers118,0352
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Insulin-degrading enzyme
D: Natriuretic peptides B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1884
Polymers118,0352
Non-polymers1542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)264.036, 264.036, 90.645
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 114560.578 Da / Num. of mol.: 2 / Fragment: UNP residues 42-1019
Mutation: C110L, E111Q, C171S, C178S, 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: HCG_1810909, IDE, RP11-366I13.1-001 / Plasmid: PPROEX-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: P14735, insulysin
#2: Protein/peptide Natriuretic peptides B / Gamma-brain natriuretic peptide


Mass: 3474.120 Da / Num. of mol.: 2 / Fragment: UNP residues 103-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPPB / References: UniProt: P16860
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.86 Å3/Da / Density % sol: 68.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEGMME-5000, 10% TACSIMATE, 10% DIOXANE, 100 mM Na-HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 14, 2009 / Details: MIRRORS
RadiationMonochromator: Si(111) AND Si(220)-SAGITALLY FOCUSED DOUBLE CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.102→50 Å / Num. all: 63372 / Num. obs: 62152 / % possible obs: 96.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.20299 / Rsym value: 0.078 / Net I/σ(I): 10.3
Reflection shellResolution: 3.102→3.182 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 1.8 / Num. unique all: 4642 / Rsym value: 0.462 / % possible all: 98.64

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3cww

3cww


Resolution: 3.102→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.517 / SU ML: 0.291 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.385
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1206 1.9 %RANDOM
Rwork0.20221 ---
obs0.203 62152 96.54 %-
all-63359 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.43 Å2 / Biso mean: 54.03 Å2 / Biso min: 36.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20.63 Å2-0 Å2
2--1.26 Å2-0 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 3.102→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15572 0 14 54 15640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02215996
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.96721641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.37551904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36324.477793
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.821152859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4831582
X-RAY DIFFRACTIONr_chiral_restr0.0830.22325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112194
X-RAY DIFFRACTIONr_mcbond_it0.3811.59552
X-RAY DIFFRACTIONr_mcangle_it0.728215464
X-RAY DIFFRACTIONr_scbond_it0.72536444
X-RAY DIFFRACTIONr_scangle_it1.3564.56175
LS refinement shellResolution: 3.102→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 76 -
Rwork0.295 4642 -
all-4718 -
obs-4642 98.64 %

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