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- PDB-6bnt: Crystal structure of AP2 mu1 adaptin C-terminal domain with IRS-1... -

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Basic information

Entry
Database: PDB / ID: 6bnt
TitleCrystal structure of AP2 mu1 adaptin C-terminal domain with IRS-1 peptide
Components
  • AP-2 complex subunit mu
  • Insulin receptor substrate 1
KeywordsENDOCYTOSIS / AP2 mu1 / IRS1
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / extrinsic component of presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD4 / AP-2 adaptor complex / IRS-related events triggered by IGF1R / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization ...Nef mediated downregulation of CD28 cell surface expression / Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / extrinsic component of presynaptic endocytic zone membrane / WNT5A-dependent internalization of FZD4 / AP-2 adaptor complex / IRS-related events triggered by IGF1R / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Retrograde neurotrophin signalling / Formation of annular gap junctions / positive regulation of synaptic vesicle endocytosis / clathrin-coated endocytic vesicle / Gap junction degradation / LDL clearance / clathrin adaptor activity / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / vesicle budding from membrane / clathrin-dependent endocytosis / insulin receptor complex / positive regulation of glucose metabolic process / Activated NTRK3 signals through PI3K / signal sequence binding / Nef Mediated CD4 Down-regulation / endolysosome membrane / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by Leptin / negative regulation of protein localization to plasma membrane / PI3K/AKT activation / cellular response to fatty acid / low-density lipoprotein particle receptor binding / Signaling by ALK / IRS activation / Recycling pathway of L1 / positive regulation of receptor internalization / synaptic vesicle endocytosis / SOS-mediated signalling / PI3K Cascade / positive regulation of glycogen biosynthetic process / EPH-ephrin mediated repulsion of cells / negative regulation of insulin secretion / Signal attenuation / phosphatidylinositol 3-kinase binding / Growth hormone receptor signaling / positive regulation of insulin receptor signaling pathway / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / negative regulation of insulin receptor signaling pathway / Interleukin-7 signaling / phosphotyrosine residue binding / SH2 domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / insulin-like growth factor receptor signaling pathway / caveola / positive regulation of glucose import / protein kinase C binding / intracellular protein transport / insulin-like growth factor receptor binding / clathrin-coated endocytic vesicle membrane / insulin receptor binding / response to insulin / receptor internalization / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / cellular response to insulin stimulus / Constitutive Signaling by Aberrant PI3K in Cancer / endocytic vesicle membrane / disordered domain specific binding / Signaling by ALK fusions and activated point mutants / signaling receptor complex adaptor activity / Cargo recognition for clathrin-mediated endocytosis / insulin receptor signaling pathway / PIP3 activates AKT signaling / glucose homeostasis / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / postsynapse / protein-containing complex assembly / transmembrane transporter binding / Potential therapeutics for SARS / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / lipid binding / positive regulation of cell population proliferation / signal transduction / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Insulin receptor substrate / Mu homology domain, subdomain B / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Phosphotyrosine-binding domain / Clathrin adaptor complexes medium chain signature 1. ...Insulin receptor substrate / Mu homology domain, subdomain B / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Phosphotyrosine-binding domain / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Insulin receptor substrate 1 / AP-2 complex subunit mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKikuchi, S. / Choi, E. / Yu, H.
Funding support United States, 1items
OrganizationGrant numberCountry
Clayton Foundation United States
CitationJournal: Nat Commun / Year: 2019
Title: Mitotic regulators and the SHP2-MAPK pathway promote IR endocytosis and feedback regulation of insulin signaling.
Authors: Choi, E. / Kikuchi, S. / Gao, H. / Brodzik, K. / Nassour, I. / Yopp, A. / Singal, A.G. / Zhu, H. / Yu, H.
History
DepositionNov 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-2 complex subunit mu
B: Insulin receptor substrate 1


Theoretical massNumber of molelcules
Total (without water)37,3592
Polymers37,3592
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-8 kcal/mol
Surface area14400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.334, 125.334, 74.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein AP-2 complex subunit mu / AP-2 mu chain / Adaptin-mu2 / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein ...AP-2 mu chain / Adaptin-mu2 / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit mu / Clathrin assembly protein complex 2 mu medium chain / Clathrin coat assembly protein AP50 / Clathrin coat-associated protein AP50 / HA2 50 kDa subunit / Plasma membrane adaptor AP-2 50 kDa protein


Mass: 35697.586 Da / Num. of mol.: 1 / Fragment: C-terminal domain (UNP residues 158-433)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP2M1, CLAPM1, KIAA0109 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96CW1
#2: Protein/peptide Insulin receptor substrate 1 / IRS-1


Mass: 1661.748 Da / Num. of mol.: 1 / Fragment: UNP residues 607-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P35568
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 4.54 Å3/Da / Density % sol: 72.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.0 M sodium malonate, pH 5.0, 0.1 M sodium acetate tri-hydrate, pH 4.5, 2% w/v PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 17, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 3.2→32.6 Å / Num. obs: 11485 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.161 / Net I/σ(I): 13.2
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.292 / Num. unique obs: 574

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BXX

1bxx


Resolution: 3.2→27.642 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.38
RfactorNum. reflection% reflection
Rfree0.2343 1113 9.97 %
Rwork0.2063 --
obs0.2092 11158 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.2→27.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 0 0 34 2084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112092
X-RAY DIFFRACTIONf_angle_d1.2312820
X-RAY DIFFRACTIONf_dihedral_angle_d12.5991290
X-RAY DIFFRACTIONf_chiral_restr0.067313
X-RAY DIFFRACTIONf_plane_restr0.008353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2002-3.34560.32991390.27751234X-RAY DIFFRACTION100
3.3456-3.52170.29031380.23881252X-RAY DIFFRACTION100
3.5217-3.74180.27671430.23021259X-RAY DIFFRACTION100
3.7418-4.02990.27651340.21541245X-RAY DIFFRACTION100
4.0299-4.4340.20611380.18991259X-RAY DIFFRACTION100
4.434-5.07220.22291360.16971252X-RAY DIFFRACTION100
5.0722-6.37740.22531380.23211274X-RAY DIFFRACTION100
6.3774-27.64340.22871470.20231270X-RAY DIFFRACTION99

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