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- PDB-5wrm: Mu2 subunit of the clathrin adaptor complex AP2 in complex with I... -

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Basic information

Entry
Database: PDB / ID: 5wrm
TitleMu2 subunit of the clathrin adaptor complex AP2 in complex with IRS-1 Y658 peptide
Components
  • AP-2 complex subunit mu
  • Insulin receptor substrate 1IRS1
KeywordsENDOCYTOSIS / clathrin adaptor AP-2 complex subunit / peptide complex
Function / homology
Function and homology information


SOS-mediated signalling / IRS-related events triggered by IGF1R / cellular response to radiation / IRS-mediated signalling / IRS activation / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling / Signaling by ALK / negative regulation of somatostatin secretion ...SOS-mediated signalling / IRS-related events triggered by IGF1R / cellular response to radiation / IRS-mediated signalling / IRS activation / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling / Signaling by ALK / negative regulation of somatostatin secretion / positive regulation of glucagon secretion / epithelial cell migration / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / Signal attenuation / WNT5A-dependent internalization of FZD4 / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / positive regulation of fatty acid beta-oxidation / phosphatidylinositol 3-kinase activator activity / vesicle budding from membrane / clathrin-dependent endocytosis / mammary gland development / insulin receptor complex / positive regulation of glucose metabolic process / signal sequence binding / transmembrane receptor protein tyrosine kinase adaptor activity / cellular response to angiotensin / RAF/MAP kinase cascade / negative regulation of protein localization to plasma membrane / response to caffeine / positive regulation of mesenchymal cell proliferation / cellular response to fatty acid / low-density lipoprotein particle receptor binding / positive regulation of epithelial cell migration / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / synaptic vesicle endocytosis / protein localization to nucleus / negative regulation of insulin secretion / positive regulation of glycogen biosynthetic process / phosphatidylinositol 3-kinase binding / lipid catabolic process / positive regulation of insulin receptor signaling pathway / positive regulation of phosphorylation / clathrin-coated pit / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor binding / phosphotyrosine residue binding / SH2 domain binding / insulin-like growth factor receptor signaling pathway / ciliary basal body / protein kinase C binding / response to activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / caveola / positive regulation of glucose import / intracellular protein transport / response to insulin / insulin receptor binding / terminal bouton / receptor internalization / cytokine-mediated signaling pathway / cellular response to insulin stimulus / disordered domain specific binding / cell migration / signaling receptor complex adaptor activity / protein-macromolecule adaptor activity / insulin receptor signaling pathway / cytoplasmic vesicle / postsynapse / regulation of gene expression / protein-containing complex assembly / transmembrane transporter binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein domain specific binding / intracellular membrane-bounded organelle / synapse / glutamatergic synapse / lipid binding / protein-containing complex binding / protein kinase binding / nucleus / plasma membrane / cytosol / cytoplasm
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 speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.597 Å
AuthorsYoneyama, Y. / Niwa, H. / Umehara, T. / Yokoyama, S. / Hakuno, F. / Takahashi, S.
CitationJournal: Elife / Year: 2018
Title: IRS-1 acts as an endocytic regulator of IGF-I receptor to facilitate sustained IGF signaling
Authors: Yoneyama, Y. / Lanzerstorfer, P. / Niwa, H. / Umehara, T. / Shibano, T. / Yokoyama, S. / Chida, K. / Weghuber, J. / Hakuno, F. / Takahashi, S.I.
History
DepositionDec 2, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)32,7012
Polymers32,7012
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-8 kcal/mol
Surface area14540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.478, 125.478, 74.138
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

#1: Protein AP-2 complex subunit mu / AP-2 mu chain / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit ...AP-2 mu chain / 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 / Mu2-adaptin / Plasma membrane adaptor AP-2 50 kDa protein


Mass: 31798.293 Da / Num. of mol.: 1 / Fragment: UNP residues 158-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Production host: Escherichia coli (E. coli) / References: UniProt: P84092
#2: Protein/peptide Insulin receptor substrate 1 / IRS1 / IRS-1 / pp185


Mass: 903.099 Da / Num. of mol.: 1 / Fragment: UNP residues 657-664 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P35570
#3: Water ChemComp-HOH / water / 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: 5.15 Å3/Da / Density % sol: 76.13 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2.3M NaCl, 0.4M Na/K Phosphate, 0.01M DTT, 15% Glycerol, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.597→50 Å / Num. obs: 20659 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rsym value: 0.09 / Net I/σ(I): 26.5
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.977 / Mean I/σ(I) obs: 1.6 / CC1/2: 0.78 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data processing
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BW8

1bw8


Resolution: 2.597→35.927 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.28
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2268 1057 5.08 %
Rwork0.1923 --
obs0.1941 20589 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.597→35.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2118 0 0 34 2152
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092161
X-RAY DIFFRACTIONf_angle_d0.9652907
X-RAY DIFFRACTIONf_dihedral_angle_d12.0731337
X-RAY DIFFRACTIONf_chiral_restr0.059321
X-RAY DIFFRACTIONf_plane_restr0.006365
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5974-2.65780.50071400.38492482X-RAY DIFFRACTION97
2.6578-2.72420.32681210.34012551X-RAY DIFFRACTION100
2.7242-2.79790.36261370.3162583X-RAY DIFFRACTION100
2.7979-2.88020.36321300.28972500X-RAY DIFFRACTION100
2.8802-2.97310.34721580.27352543X-RAY DIFFRACTION100
2.9731-3.07930.31531280.25172564X-RAY DIFFRACTION100
3.0793-3.20250.32921300.24372529X-RAY DIFFRACTION100
3.2025-3.34820.26071510.22782531X-RAY DIFFRACTION100
3.3482-3.52450.23421310.20122544X-RAY DIFFRACTION99
3.5245-3.74510.22391290.19232559X-RAY DIFFRACTION100
3.7451-4.0340.19371500.17662532X-RAY DIFFRACTION100
4.034-4.43920.20631520.14622516X-RAY DIFFRACTION100
4.4392-5.08010.15481310.13092527X-RAY DIFFRACTION100
5.0801-6.39450.1791150.17752579X-RAY DIFFRACTION100
6.3945-35.93080.20451370.17882541X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.67560.04781.09687.08650.9461.2320.38330.0789-0.2646-0.8153-0.52951.3138-0.0968-0.35070.24220.56180.0688-0.07270.6536-0.08850.683749.05928.028728.3978
24.77183.55352.28868.49743.04343.194-0.1070.00480.20810.2664-0.03940.0682-0.02120.00430.11930.5588-0.0520.04970.62130.08640.425566.373729.29950.0597
33.12053.72042.63034.37753.12072.207-0.21610.74042.09420.0214-0.97752.6134-0.49370.13171.19920.8607-0.0867-0.21950.86640.11641.607565.565447.653343.7124
41.8062-2.89050.14884.63361.07421.07260.26440.0064-0.3368-0.2319-0.27880.66750.0534-0.16790.08390.5849-0.07590.07380.6334-0.03910.655852.63356.462735.1003
52.25681.72341.99692.2415-0.83357.75910.2441-1.30780.06981.138-0.70140.87790.8661-0.66250.47810.8655-0.11020.05620.8508-0.10490.80955.0057-1.195138.8591
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 159 through 286 )
2X-RAY DIFFRACTION2chain 'A' and (resid 287 through 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 386 )
4X-RAY DIFFRACTION4chain 'A' and (resid 387 through 435 )
5X-RAY DIFFRACTION5chain 'P' and (resid 1 through 6 )

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