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- PDB-1i31: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 CLATHRIN ADAPTOR, COMPLEXED WIT... -

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Basic information

Entry
Database: PDB / ID: 1i31
TitleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 CLATHRIN ADAPTOR, COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM AT 2.5 A RESOLUTION
Components
  • CLATHRIN COAT ASSEMBLY PROTEIN AP50
  • EPIDERMAL GROWTH FACTOR RECEPTOR
KeywordsENDOCYTOSIS/EXOCYTOSIS / beta-sandwich / peptide-binding site / protein-peptide complex / clathrin adaptor / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ...Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / regulation of JNK cascade / multivesicular body, internal vesicle lumen / positive regulation of prolactin secretion / negative regulation of cardiocyte differentiation / response to hydroxyisoflavone / diterpenoid metabolic process / ovulation cycle / positive regulation of mucus secretion / epidermal growth factor binding / response to UV-A / tongue development / midgut development / ERBB2-EGFR signaling pathway / digestive tract morphogenesis / hydrogen peroxide metabolic process / low-density lipoprotein particle receptor binding / morphogenesis of an epithelial fold / response to lipid / transmembrane receptor protein tyrosine kinase activator activity / cellular response to cadmium ion / intracellular vesicle / response to cobalamin / eyelid development in camera-type eye / negative regulation of epidermal growth factor receptor signaling pathway / cerebral cortex cell migration / Trafficking of GluR2-containing AMPA receptors / protein tyrosine kinase activator activity / positive regulation of receptor internalization / negative regulation of mitotic cell cycle / synaptic vesicle endocytosis / endocytic vesicle / hair follicle development / positive regulation of G1/S transition of mitotic cell cycle / epidermis development / embryonic placenta development / positive regulation of bone resorption / negative regulation of protein localization to plasma membrane / positive regulation of phosphorylation / regulation of ERK1 and ERK2 cascade / salivary gland morphogenesis / clathrin-coated pit / positive regulation of glial cell proliferation / positive regulation of vasoconstriction / transmembrane receptor protein tyrosine kinase activity / receptor-mediated endocytosis / positive regulation of DNA repair / cellular response to dexamethasone stimulus / positive regulation of synaptic transmission, glutamatergic / neuron projection morphogenesis / basal plasma membrane / positive regulation of epithelial cell proliferation / liver development / positive regulation of superoxide anion generation / liver regeneration / epithelial cell proliferation / neurogenesis / positive regulation of DNA replication / cellular response to reactive oxygen species / positive regulation of protein localization to plasma membrane / astrocyte activation / epidermal growth factor receptor activity / intracellular protein transport / positive regulation of smooth muscle cell proliferation / cellular response to amino acid stimulus / lung development / cellular response to estradiol stimulus / synaptic membrane / epidermal growth factor receptor signaling pathway / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to growth factor stimulus / terminal bouton / receptor protein-tyrosine kinase / negative regulation of protein catabolic process / cell morphogenesis / : / cell-cell adhesion / receptor internalization / positive regulation of miRNA transcription / kinase binding
Similarity search - Function
Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain ...Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / receptor protein-tyrosine kinase / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsModis, Y. / Boll, W. / Rapoport, I. / Kirchhausen, T.
Citation
Journal: To be Published
Title: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 CLATHRIN ADAPTOR, COMPLEXED WITH EGFR INTERNALIZATION PEPTIDE FYRALM AT 2.5 A RESOLUTION
Authors: Modis, Y. / Boll, W. / Rapoport, I. / Kirchhausen, T.
#1: Journal: Science / Year: 1998
Title: A Structural Explanation for the Recognition of Tyrosine-Based Endocytic Signals
Authors: Owen, D.J. / Evans, P.R.
History
DepositionFeb 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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: CLATHRIN COAT ASSEMBLY PROTEIN AP50
P: EPIDERMAL GROWTH FACTOR RECEPTOR


Theoretical massNumber of molelcules
Total (without water)36,5482
Polymers36,5482
Non-polymers00
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint-5 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.727, 125.727, 74.634
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-11-

HOH

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Components

#1: Protein CLATHRIN COAT ASSEMBLY PROTEIN AP50 / MU2 ADAPTIN OF AP2 ADAPTOR


Mass: 35746.543 Da / Num. of mol.: 1 / Fragment: RESIDUES 122-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: AP50 / Plasmid: PPROEX / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P84092
#2: Protein/peptide EPIDERMAL GROWTH FACTOR RECEPTOR / EGFR


Mass: 800.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 998-1003 / Source method: obtained synthetically
Details: The hexapeptide of epidermal growth factor receptor was chemically synthesized
References: GenBank: 6478868, UniProt: A8IP97*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 4.66 Å3/Da / Density % sol: 73.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: SODIUM FORMATE, SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.006 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2000 / Details: BENT CYLINDRICAL SI-MIRROR (RH COATING)
RadiationMonochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 21919 / Num. obs: 21919 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 50.8 % / Biso Wilson estimate: 74.6 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.8
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 6 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.6 / % possible all: 76.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BW8

1bw8


Resolution: 2.5→20 Å
Isotropic thermal model: ISOTROPIC ATOMIC TEMPERATURE FACTORS
Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: MINIMIZATION OF MAXIMUM LIKELIHOOD RESIDUAL BY CONJUGATE DIRECTION METHOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2547 1123 5 %RANDOM
Rwork0.2466 ---
all-21919 --
obs-20796 96.4 %-
Displacement parametersBiso mean: -0.01087 Å2
Baniso -1Baniso -2Baniso -3
1-1.214 Å20 Å20.267 Å2
2--0.268 Å20 Å2
3----1.095 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21384 Å0.27134 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 47 2169
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.019
X-RAY DIFFRACTIONp_angle_d0.0550.055
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.050.061
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.4872
X-RAY DIFFRACTIONp_mcangle_it4.0213
X-RAY DIFFRACTIONp_scbond_it3.4692
X-RAY DIFFRACTIONp_scangle_it5.2133
X-RAY DIFFRACTIONp_plane_restr0.0251
X-RAY DIFFRACTIONp_chiral_restr0.2040.15
X-RAY DIFFRACTIONp_singtor_nbd0.2150.3
X-RAY DIFFRACTIONp_multtor_nbd0.2670.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1780.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.73
X-RAY DIFFRACTIONp_staggered_tor19.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor21.520
X-RAY DIFFRACTIONp_special_tor
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-ID% reflection obs (%)
2.522-2.6370.4741150.39X-RAY DIFFRACTION79.3
2.637-2.7640.3261230.283X-RAY DIFFRACTION91.1

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