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

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Basic information

Entry
Database: PDB / ID: 5wrk
TitleMu2 subunit of the clathrin adaptor complex AP2 in complex with IRS-1 Y608 peptide
Components
  • AP-2 complex subunit mu
  • Insulin receptor substrate 1
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 / Interleukin-7 signaling / IRS activation / Signaling by LTK / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling ...SOS-mediated signalling / IRS-related events triggered by IGF1R / cellular response to radiation / IRS-mediated signalling / Interleukin-7 signaling / IRS activation / Signaling by LTK / PI3K/AKT activation / PI3K Cascade / PIP3 activates AKT signaling / Signaling by ALK / negative regulation of somatostatin secretion / positive regulation of glucagon secretion / Gap junction degradation / Formation of annular gap junctions / epithelial cell migration / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / Signal attenuation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / positive regulation of glucose metabolic process / Recycling pathway of L1 / positive regulation of fatty acid beta-oxidation / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / phosphatidylinositol 3-kinase activator activity / vesicle budding from membrane / clathrin-dependent endocytosis / insulin receptor complex / signal sequence binding / transmembrane receptor protein tyrosine kinase adaptor activity / mammary gland development / cellular response to fatty acid / RAF/MAP kinase cascade / response to caffeine / positive regulation of mesenchymal cell proliferation / low-density lipoprotein particle receptor binding / Trafficking of GluR2-containing AMPA receptors / cellular response to angiotensin / positive regulation of receptor internalization / positive regulation of epithelial cell migration / positive regulation of phosphorylation / synaptic vesicle endocytosis / protein localization to nucleus / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / negative regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase binding / lipid catabolic process / cellular response to brain-derived neurotrophic factor stimulus / insulin-like growth factor receptor binding / phosphotyrosine residue binding / clathrin-coated pit / signaling adaptor activity / negative regulation of insulin receptor signaling pathway / insulin-like growth factor receptor signaling pathway / SH2 domain binding / protein kinase C binding / response to activity / positive regulation of D-glucose import across plasma membrane / insulin receptor binding / intracellular protein transport / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of insulin secretion / response to insulin / caveola / receptor internalization / cellular response to insulin stimulus / cytokine-mediated signaling pathway / terminal bouton / disordered domain specific binding / synaptic vesicle / insulin receptor signaling pathway / cell migration / signaling receptor complex adaptor activity / regulation of gene expression / protein-containing complex assembly / cytoplasmic vesicle / response to ethanol / protein-macromolecule adaptor activity / transmembrane transporter binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / ciliary basal body / protein domain specific binding / intracellular membrane-bounded organelle / synapse / lipid binding / protein kinase binding / protein-containing complex binding
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Mu homology domain, subdomain B / 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 ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / Mu homology domain, subdomain B / 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. / : / IRS-type PTB domain / PTB domain (IRS-1 type) / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / 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
NICKEL (II) ION / Insulin receptor substrate 1 / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8684
Polymers31,7512
Non-polymers1172
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area830 Å2
ΔGint-14 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.065, 126.065, 73.403
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 / 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: 30911.723 Da / Num. of mol.: 1 / Fragment: UNP residues 158-223,UNP residues 261-435
Source method: isolated from a genetically manipulated source
Details: B chain is a part of A chain for which residue names and residue numbers were not determined due to insufficient electron density
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 / IRS-1 / pp185


Mass: 838.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P35570
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
Sequence detailsTHE ELECTRON DENSITY OF RESIDUES A224-A260 IS WEAK. FIVE RESIDUES WERE PLACED BUT THEIR RESIDUE ...THE ELECTRON DENSITY OF RESIDUES A224-A260 IS WEAK. FIVE RESIDUES WERE PLACED BUT THEIR RESIDUE NUMBERS A227-A231 ARE NOT CONCLUSIVE AND LABELED UNK. REAL SEQUENCE FOR RESIDUES A224-A260 SHOULD BE KQGKGTADETSKSGKQSIAIDDCTFHQCVRLSKFDSE.

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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: 5.3 Å3/Da / Density % sol: 73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.4M Na formate, 0.05M NiCl, 0.1M Na acetate pH 6.0

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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 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.624→50 Å / Num. obs: 20035 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rsym value: 0.075 / Net I/σ(I): 28.1
Reflection shellResolution: 2.63→2.68 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.433 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

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

1bw8


Resolution: 2.62→43.8 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 26.64
RfactorNum. reflection% reflection
Rfree0.223 1019 5.12 %
Rwork0.185 --
obs0.187 19977 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.62→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 2 0 2005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082043
X-RAY DIFFRACTIONf_angle_d0.9482748
X-RAY DIFFRACTIONf_dihedral_angle_d13.7351268
X-RAY DIFFRACTIONf_chiral_restr0.059305
X-RAY DIFFRACTIONf_plane_restr0.006343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6238-2.68940.39471480.34892569X-RAY DIFFRACTION98
2.6894-2.76210.37371690.32882641X-RAY DIFFRACTION100
2.7621-2.84330.34091560.30112599X-RAY DIFFRACTION100
2.8433-2.93510.30461460.27592651X-RAY DIFFRACTION100
2.9351-3.040.31111320.27122659X-RAY DIFFRACTION100
3.04-3.16170.32421410.26282651X-RAY DIFFRACTION100
3.1617-3.30550.29841430.23842616X-RAY DIFFRACTION100
3.3055-3.47970.23711780.20722623X-RAY DIFFRACTION100
3.4797-3.69760.22621540.18932619X-RAY DIFFRACTION100
3.6976-3.9830.20071360.16922632X-RAY DIFFRACTION100
3.983-4.38340.20551450.1422653X-RAY DIFFRACTION100
4.3834-5.01690.16971020.1262676X-RAY DIFFRACTION100
5.0169-6.31780.15391090.1742690X-RAY DIFFRACTION100
6.3178-43.8090.20471310.17692633X-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)
14.28450.66641.31133.7849-0.45727.44590.79550.791-0.266-1.3909-0.43880.40690.5130.457-0.35051.1270.2057-0.26250.952-0.16891.000556.331-8.325218.1225
22.15330.44071.21794.24440.02990.76850.0408-0.2137-0.08970.2197-0.18920.9618-0.12970.00540.15170.696-0.05060.11060.642-0.05630.594753.739818.293237.2121
32.1067-1.84430.22033.1936-0.31291.96510.59130.3192-0.313-0.6662-0.39650.41910.27470.0003-0.15320.78160.1182-0.09620.8623-0.06890.869151.17986.387227.5053
41.7631-1.49210.70912.64650.31032.13760.11070.0545-0.7983-0.0185-0.16751.37260.6826-0.619-0.17980.96750.0472-0.23280.8924-0.14761.218244.2286.43125.769
51.28460.08931.56532.63180.52971.8760.07510.01620.1347-0.4126-0.23020.4813-0.4748-0.10910.05830.7401-0.01630.14430.8761-0.06110.738553.63522.3538.628
64.02531.11772.18773.9092.19732.9443-0.158-0.0623-0.24170.3133-0.0802-0.23660.02550.15740.23360.6923-0.0740.09310.62110.09150.536967.76628.682148.7458
72.46451.1111.63780.62711.0541.8239-0.86270.06370.9281-0.8014-0.41490.4194-0.4550.46830.95041.1002-0.1708-0.41040.75530.12551.135866.10847.80342.967
82.65051.34352.2985.42192.85432.5650.61310.3118-0.20070.935-0.1696-0.3740.368-0.04680.13360.7476-0.03810.20530.7126-0.09050.776754.26214.35739.544
91.3966-0.8240.92872.91520.83281.17790.47770.0527-0.3715-0.3017-0.42250.88360.138-0.1672-0.04420.7658-0.023-0.04750.7908-0.13750.953952.5242.95431.982
105.60942.93210.07169.0163-1.74189.34790.2506-1.30630.16740.7058-1.18650.54870.0992-0.04780.88220.7701-0.06410.02640.8376-0.00770.841455.6295-0.576938.1658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 159 THROUGH 171 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 172 THROUGH 190 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 191 THROUGH 215 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 216 THROUGH 269 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 270 THROUGH 296 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 297 THROUGH 372 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 373 THROUGH 386 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 387 THROUGH 402 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 403 THROUGH 435 )
10X-RAY DIFFRACTION10CHAIN 'P' AND (RESID 1 THROUGH 6 )

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