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- PDB-4ral: Crystal structure of insulin degrading enzyme in complex with mac... -

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Basic information

Entry
Database: PDB / ID: 4ral
TitleCrystal structure of insulin degrading enzyme in complex with macrophage inflammatory protein 1 beta
Components
  • C-C motif chemokine 4
  • Insulin-degrading enzyme
KeywordsHYDROLASE/CYTOKINE / IDE / MIP1alpha / metal-binding / metalloprotease / chemotaxis / inflammatory response / HYDROLASE-CYTOKINE complex
Function / homology
Function and homology information


CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / CCR5 chemokine receptor binding / CCR chemokine receptor binding / insulin metabolic process / amyloid-beta clearance by cellular catabolic process ...CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / insulysin / beta-endorphin binding / ubiquitin recycling / insulin catabolic process / CCR5 chemokine receptor binding / CCR chemokine receptor binding / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / chemokine-mediated signaling pathway / eosinophil chemotaxis / cytosolic proteasome complex / positive regulation of calcium ion transport / chemokine activity / Chemokine receptors bind chemokines / insulin binding / regulation of aerobic respiration / peptide catabolic process / establishment or maintenance of cell polarity / Interleukin-10 signaling / amyloid-beta clearance / peroxisomal matrix / host-mediated suppression of viral transcription / amyloid-beta metabolic process / positive regulation of protein binding / Insulin receptor recycling / negative regulation of proteolysis / peptide binding / positive regulation of calcium-mediated signaling / proteolysis involved in protein catabolic process / cytokine activity / Peroxisomal protein import / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / response to toxic substance / response to virus / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of protein catabolic process / insulin receptor signaling pathway / peroxisome / cell-cell signaling / amyloid-beta binding / virus receptor activity / endopeptidase activity / G alpha (i) signalling events / basolateral plasma membrane / cell adhesion / Ub-specific processing proteases / immune response / positive regulation of cell migration / inflammatory response / external side of plasma membrane / 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 / 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 / : / 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
C-C motif chemokine 4 / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.148 Å
AuthorsLiang, W.G. / Ren, M. / Guo, Q. / Tang, W.J.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme.
Authors: Liang, W.G. / Ren, M. / Zhao, F. / Tang, W.J.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2015ID: 4QLD
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

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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
D: C-C motif chemokine 4
E: C-C motif chemokine 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,9016
Polymers244,7714
Non-polymers1312
Water1,20767
1
A: Insulin-degrading enzyme
D: C-C motif chemokine 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4513
Polymers122,3852
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-50 kcal/mol
Surface area38000 Å2
MethodPISA
2
B: Insulin-degrading enzyme
E: C-C motif chemokine 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,4513
Polymers122,3852
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-48 kcal/mol
Surface area38600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)263.117, 263.117, 90.850
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 / Abeta-degrading protease / Insulin protease / Insulinase / Insulysin


Mass: 114560.578 Da / Num. of mol.: 2 / Fragment: UNP 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 / Production host: Escherichia coli (E. coli) / References: UniProt: P14735, insulysin
#2: Protein C-C motif chemokine 4 / G-26 T-lymphocyte-secreted protein / HC21 / Lymphocyte activation gene 1 protein / LAG-1 / MIP-1- ...G-26 T-lymphocyte-secreted protein / HC21 / Lymphocyte activation gene 1 protein / LAG-1 / MIP-1-beta(1-69) / Macrophage inflammatory protein 1-beta / MIP-1-beta / PAT 744 / Protein H400 / SIS-gamma / Small-inducible cytokine A4 / T-cell activation protein 2 / ACT-2 / MIP-1-beta(3-69)


Mass: 7824.742 Da / Num. of mol.: 2 / Fragment: UNP residues 24-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCL4, LAG1, MIP1B, SCYA4 / Production host: Escherichia coli (E. coli) / References: UniProt: P13236
#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.: 67 / 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: 3.71 Å3/Da / Density % sol: 66.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 13% PEG5000 MME, 100 mM HEPES, pH 7.0, 10% Tacsimate, 10% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 8, 2010
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.148→48.263 Å / Num. all: 59484 / Num. obs: 59484 / % possible obs: 95.5 % / Observed criterion σ(F): 3.06 / Observed criterion σ(I): 3.06 / Redundancy: 4.3 % / Rmerge(I) obs: 0.209 / Rsym value: 0.216 / Net I/σ(I): 7.4
Reflection shellHighest resolution: 3.148 Å

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CWW

3cww


Resolution: 3.148→48.263 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 851 1.16 %RANDOM
Rwork0.1911 ---
obs0.1918 59484 60.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.148→48.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15757 0 2 67 15826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416146
X-RAY DIFFRACTIONf_angle_d0.84821830
X-RAY DIFFRACTIONf_dihedral_angle_d13.9566110
X-RAY DIFFRACTIONf_chiral_restr0.0332347
X-RAY DIFFRACTIONf_plane_restr0.0042826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.148-3.34560.29491090.23658802X-RAY DIFFRACTION44
3.3456-3.60380.28791200.22239966X-RAY DIFFRACTION50
3.6038-3.96630.27961260.204210353X-RAY DIFFRACTION52
3.9663-4.53990.25411330.18111763X-RAY DIFFRACTION59
4.5399-5.71830.22881610.176315066X-RAY DIFFRACTION75
5.7183-48.26890.24272020.181916332X-RAY DIFFRACTION81
Refinement TLS params.Method: refined / Origin x: -104.0282 Å / Origin y: 23.6136 Å / Origin z: -5.9716 Å
111213212223313233
T0.3973 Å2-0.0157 Å20.0278 Å2-0.3248 Å20.0657 Å2--0.3885 Å2
L0.0707 °2-0.0207 °20.0046 °2-0.5388 °20.3373 °2--0.248 °2
S-0.0256 Å °0.0062 Å °0.0051 Å °0.0064 Å °0.0272 Å °-0.0011 Å °0.0794 Å °0.0301 Å °-0.0033 Å °
Refinement TLS groupSelection details: all

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