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- PDB-9fix: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -

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Basic information

Entry
Database: PDB / ID: 9fix
TitleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRPYSYRHFA
Components
  • AP-2 complex subunit mu
  • Low-density lipoprotein receptor-related protein 6
KeywordsSIGNALING PROTEIN / WNT / endocytosis / signalosome
Function / homology
Function and homology information


Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / neural crest formation / LDL clearance / Retrograde neurotrophin signalling / Signaling by RNF43 mutants / VLDLR internalisation and degradation ...Wnt-Frizzled-LRP5/6 complex / Negative regulation of TCF-dependent signaling by WNT ligand antagonists / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / neural crest formation / LDL clearance / Retrograde neurotrophin signalling / Signaling by RNF43 mutants / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / kinase inhibitor activity / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / toxin transmembrane transporter activity / regulation of vesicle size / Wnt receptor activity / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / low-density lipoprotein particle receptor activity / Wnt-protein binding / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / cellular response to cholesterol / vesicle budding from membrane / clathrin-dependent endocytosis / midbrain dopaminergic neuron differentiation / signal sequence binding / dopaminergic neuron differentiation / frizzled binding / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / neural crest cell differentiation / low-density lipoprotein particle receptor binding / negative regulation of smooth muscle cell apoptotic process / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / protein serine/threonine kinase inhibitor activity / synaptic vesicle endocytosis / canonical Wnt signaling pathway / negative regulation of protein localization to plasma membrane / coreceptor activity / positive regulation of cell cycle / clathrin-coated pit / Regulation of FZD by ubiquitination / TCF dependent signaling in response to WNT / protein localization to plasma membrane / intracellular protein transport / cell-cell adhesion / response to peptide hormone / receptor internalization / Wnt signaling pathway / endocytosis / terminal bouton / disordered domain specific binding / synaptic vesicle / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / cytoplasmic vesicle / early endosome membrane / chemical synaptic transmission / transmembrane transporter binding / postsynapse / membrane raft / signaling receptor binding / neuronal cell body / synapse / lipid binding / positive regulation of DNA-templated transcription / glutamatergic synapse / cell surface / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Low density lipoprotein receptor-related protein 5/6 / : / 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 ...Low density lipoprotein receptor-related protein 5/6 / : / 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 / 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. / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Longin-like domain superfamily / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / Epidermal growth factor-like domain. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 6 / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsRenko, M. / Gammons, M.V. / Bienz, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: To Be Published
Title: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH LRP6 INTERNALIZATION PEPTIDE SYRPYSYRHFA
Authors: Gammons, M.V.
History
DepositionMay 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Low-density lipoprotein receptor-related protein 6
M: AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)34,3392
Polymers34,3392
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-5 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.796, 125.796, 73.766
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/peptide Low-density lipoprotein receptor-related protein 6 / LRP-6


Mass: 1449.593 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O75581
#2: 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: 32889.559 Da / Num. of mol.: 1
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
Has protein modificationN

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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: 4.91 Å3/Da / Density % sol: 74.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2.0-2.2 M NaCl 0.4M Na/K phosphate 0.1M MES PH 7.1 15-20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: May 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.78→47.91 Å / Num. obs: 16878 / % possible obs: 99.7 % / Redundancy: 20.8 % / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.035 / Rrim(I) all: 0.11 / Net I/σ(I): 19.8
Reflection shellResolution: 2.78→2.93 Å / Rmerge(I) obs: 1.75 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2454 / Rpim(I) all: 0.56 / Rrim(I) all: 1.84

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→47.91 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.534 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23342 842 5 %RANDOM
Rwork0.19662 ---
obs0.19843 16018 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.539 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.78→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 0 0 2089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122134
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162115
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.852873
X-RAY DIFFRACTIONr_angle_other_deg0.6161.7734876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2815256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.453518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.86110398
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022444
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02488
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.3138.3651036
X-RAY DIFFRACTIONr_mcbond_other8.3148.3641036
X-RAY DIFFRACTIONr_mcangle_it11.28914.9851288
X-RAY DIFFRACTIONr_mcangle_other11.29314.9891289
X-RAY DIFFRACTIONr_scbond_it9.99.1921098
X-RAY DIFFRACTIONr_scbond_other9.8979.1951099
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.03616.5121586
X-RAY DIFFRACTIONr_long_range_B_refined16.94381.452146
X-RAY DIFFRACTIONr_long_range_B_other16.94181.472147
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.78→2.85 Å
RfactorNum. reflection% reflection
Rfree0.404 64 -
Rwork0.388 1184 -
obs--99.05 %

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