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- PDB-3h44: Crystal Structure of Insulin Degrading Enzyme in Complex with mac... -

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Basic information

Entry
Database: PDB / ID: 3h44
TitleCrystal Structure of Insulin Degrading Enzyme in Complex with macrophage inflammatory protein 1 alpha
Components
  • C-C motif chemokine 3
  • Insulin-degrading enzyme
KeywordsHydrolase/Cytokine / IDE / MIP1alpha / Cytoplasm / Hydrolase / Metal-binding / Metalloprotease / Polymorphism / Protease / Zinc / Chemotaxis / Cytokine / Disulfide bond / Inflammatory response / Secreted / Hydrolase-Cytokine COMPLEX
Function / homology
Function and homology information


granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / positive regulation of microglial cell migration / insulysin / beta-endorphin binding / astrocyte cell migration / ubiquitin recycling / regulation of behavior ...granulocyte chemotaxis / lymphocyte chemotaxis / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / positive regulation of microglial cell migration / insulysin / beta-endorphin binding / astrocyte cell migration / ubiquitin recycling / regulation of behavior / insulin catabolic process / CCR5 chemokine receptor binding / eosinophil degranulation / regulation of sensory perception of pain / CCR chemokine receptor binding / insulin metabolic process / signaling / negative regulation of bone mineralization / positive regulation of microglial cell activation / amyloid-beta clearance by cellular catabolic process / cell activation / hormone catabolic process / bradykinin catabolic process / T cell chemotaxis / chemokine-mediated signaling pathway / eosinophil chemotaxis / response to cholesterol / cytosolic proteasome complex / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / insulin binding / regulation of aerobic respiration / phospholipase activator activity / peptide catabolic process / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / negative regulation of osteoclast differentiation / Interleukin-10 signaling / exocytosis / monocyte chemotaxis / amyloid-beta clearance / peroxisomal matrix / cellular response to interleukin-1 / host-mediated suppression of viral transcription / amyloid-beta metabolic process / positive regulation of protein binding / Insulin receptor recycling / negative regulation of proteolysis / neutrophil chemotaxis / cytoskeleton organization / peptide binding / positive regulation of calcium-mediated signaling / proteolysis involved in protein catabolic process / positive regulation of interleukin-1 beta production / cell chemotaxis / Peroxisomal protein import / protein catabolic process / calcium-mediated signaling / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / cellular response to type II interferon / response to toxic substance / intracellular calcium ion homeostasis / chemotaxis / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of protein catabolic process / antimicrobial humoral immune response mediated by antimicrobial peptide / osteoblast differentiation / cellular response to tumor necrosis factor / kinase activity / calcium ion transport / insulin receptor signaling pathway / peroxisome / cell-cell signaling / positive regulation of neuron apoptotic process / MAPK cascade / regulation of cell shape / amyloid-beta binding / virus receptor activity / endopeptidase activity / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / Ub-specific processing proteases / positive regulation of cell migration / inflammatory response / negative regulation of gene expression / external side of plasma membrane / positive regulation of gene expression / protein-containing complex binding / cell surface / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / proteolysis
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Chemokine beta/gamma/delta ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 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 / C-C motif chemokine 3 / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRen, M. / Guo, Q. / Tang, W.J.
CitationJournal: To be Published
Title: Macrophage Inflammatory Protein-1 Is A Novel High Affinity Substrate For Human Insulin Degrading Enzyme
Authors: Ren, M. / Guo, Q. / Tang, W.J.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: C-C motif chemokine 3
D: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,36812
Polymers244,7084
Non-polymers6598
Water2,396133
1
A: Insulin-degrading enzyme
C: C-C motif chemokine 3
hetero molecules

B: Insulin-degrading enzyme
D: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,36812
Polymers244,7084
Non-polymers6598
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/61
Buried area7950 Å2
ΔGint-53 kcal/mol
Surface area73400 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-49 kcal/mol
Surface area74830 Å2
MethodPISA
3
A: Insulin-degrading enzyme
C: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6846
Polymers122,3542
Non-polymers3304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-24 kcal/mol
Surface area38170 Å2
MethodPISA
4
B: Insulin-degrading enzyme
D: C-C motif chemokine 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,6846
Polymers122,3542
Non-polymers3304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-22 kcal/mol
Surface area38150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)262.737, 262.737, 90.502
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: 114560.578 Da / Num. of mol.: 2 / Fragment: residues 42-1019
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: proEX-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P14735, insulysin
#2: Protein C-C motif chemokine 3 / Small-inducible cytokine A3 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / Tonsillar ...Small-inducible cytokine A3 / Macrophage inflammatory protein 1-alpha / MIP-1-alpha / Tonsillar lymphocyte LD78 alpha protein / G0/G1 switch regulatory protein 19-1 / G0S19-1 protein / SIS-beta / PAT 464.1 / LD78-alpha


Mass: 7793.664 Da / Num. of mol.: 2 / Fragment: residues 23-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL3, G0S19-1, MIP1A, MIP1alpha, SCYA3 / Plasmid: pET-32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10147
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 133 / 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: 3.68 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEGMME 5000, 100mM HEPES, pH 7.0, 10%, Tacsimate, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2008 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 67989 / Num. obs: 67744 / % possible obs: 99.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.142 / Rsym value: 0.142
Reflection shellResolution: 3→3.11 Å / Redundancy: 5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / Rsym value: 0.514 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0044refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2wby

2wby


Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.005 / SU ML: 0.249 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 1.096 / ESU R Free: 0.351 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3612 5.1 %RANDOM
Rwork0.183 ---
obs0.185 67744 99.6 %-
all-67989 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å2-0 Å2
2--0.8 Å2-0 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15766 0 38 133 15937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02216153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.96921826
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48851918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97724.501802
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.561152897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6891585
X-RAY DIFFRACTIONr_chiral_restr0.1070.22347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112267
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5231.59642
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.066215594
X-RAY DIFFRACTIONr_scbond_it1.69436511
X-RAY DIFFRACTIONr_scangle_it3.0244.56232
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 274 -
Rwork0.259 4862 -
obs--98.11 %

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