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- PDB-3ml6: a complex between Dishevelled2 and clathrin adaptor AP-2 -

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Basic information

Entry
Database: PDB / ID: 3ml6
Titlea complex between Dishevelled2 and clathrin adaptor AP-2
ComponentsChimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu
KeywordsPROTEIN TRANSPORT / Dishevelled / AP2 / Frizzled internalization / non-canonical Wnt signaling
Function / homology
Function and homology information


WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / Signaling by Hippo / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / segmentation / Asymmetric localization of PCP proteins / Gap junction degradation / Formation of annular gap junctions ...WNT mediated activation of DVL / convergent extension involved in organogenesis / PCP/CE pathway / Signaling by Hippo / convergent extension involved in neural plate elongation / Disassembly of the destruction complex and recruitment of AXIN to the membrane / segmentation / Asymmetric localization of PCP proteins / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Degradation of DVL / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / segment specification / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / positive regulation of neuron projection arborization / regulation of vesicle size / RHO GTPases Activate Formins / non-canonical Wnt signaling pathway / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / cochlea morphogenesis / Recycling pathway of L1 / Clathrin-mediated endocytosis / 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 / frizzled binding / clathrin-coated vesicle / Wnt signaling pathway, planar cell polarity pathway / aggresome / low-density lipoprotein particle receptor binding / heart looping / Trafficking of GluR2-containing AMPA receptors / outflow tract morphogenesis / positive regulation of receptor internalization / positive regulation of GTPase activity / lateral plasma membrane / positive regulation of signal transduction by p53 class mediator / synaptic vesicle endocytosis / canonical Wnt signaling pathway / negative regulation of protein localization to plasma membrane / heart morphogenesis / clathrin-coated pit / neural tube closure / positive regulation of JNK cascade / intracellular protein transport / receptor internalization / small GTPase binding / Wnt signaling pathway / terminal bouton / apical part of cell / disordered domain specific binding / synaptic vesicle / intracellular protein localization / regulation of cell population proliferation / heart development / protein-containing complex assembly / cytoplasmic vesicle / cell cortex / protein-macromolecule adaptor activity / transmembrane transporter binding / cytoskeleton / postsynapse / intracellular signal transduction / nuclear body / protein domain specific binding / synapse / lipid binding / protein kinase binding / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain ...Dishevelled-2 / Dishevelled protein domain / Dishevelled family / Dishevelled C-terminal / Dishevelled specific domain / Segment polarity protein dishevelled (Dsh) C terminal / Dishevelled-related protein / DIX domain / DIX domain superfamily / DIX domain / DIX domain profile. / Domain present in Dishevelled and axin / 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. / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Longin-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
AP-2 complex subunit mu / Segment polarity protein dishevelled homolog DVL-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsYu, A. / Xing, Y. / Harrison, S.C. / Kirchhausen, T.L.
CitationJournal: Structure / Year: 2010
Title: Structural analysis of the interaction between Dishevelled2 and clathrin AP-2 adaptor, a critical step in noncanonical Wnt signaling.
Authors: Yu, A. / Xing, Y. / Harrison, S.C. / Kirchhausen, T.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jan 24, 2018Group: Refinement description / Category: refine / Item: _refine.pdbx_starting_model
Revision 1.4Dec 26, 2018Group: Data collection / Structure summary / Category: entity / struct
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _struct.pdbx_descriptor / _struct.title
Revision 1.5Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu
B: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu
C: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu
D: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu
E: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu
F: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)260,4206
Polymers260,4206
Non-polymers00
Water00
1
A: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)43,4031
Polymers43,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)43,4031
Polymers43,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)43,4031
Polymers43,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)43,4031
Polymers43,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)43,4031
Polymers43,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Theoretical massNumber of molelcules
Total (without water)43,4031
Polymers43,4031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)292.371, 98.137, 171.322
Angle α, β, γ (deg.)90.00, 121.97, 90.00
Int Tables number5
Space group name H-MC121
Detailsnone

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Components

#1: Protein
Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu


Mass: 43403.367 Da / Num. of mol.: 6
Fragment: PROTEIN Dishevelled2 (UNP RESIDUES 417-510), AP-2 COMPLEX 2 MU SUBUNIT (UNP RESIDUES 170-435)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Rattus norvegicus (Norway rat)
Gene: Dishevlled2, u2 / Plasmid: pPROEX-HTC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q60838, UniProt: P84092
Sequence detailsTHE STRUCTURE IS REPRESENTATIVE OF A CHIMERIC PROTEIN BETWEEN DISHEVLLED2 AND CLATHRIN ADAPTOR AP-2 ...THE STRUCTURE IS REPRESENTATIVE OF A CHIMERIC PROTEIN BETWEEN DISHEVLLED2 AND CLATHRIN ADAPTOR AP-2 JOINED BY A LINKER AS SPECIFIED IN REMARK SEQADV

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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 Å3/Da / Density % sol: 69.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.7 M K/Na tartrate, 0.1 M sodium citrate, pH 5.5, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. all: 51791 / Num. obs: 51429 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 11.3
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2485 / Rsym value: 0.774 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BW8, 1FSH

1bw8

1fsh


Resolution: 3.5→49.07 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 5714272.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.335 2576 5 %RANDOM
Rwork0.308 ---
obs0.308 51395 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0607 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 117.5 Å2
Baniso -1Baniso -2Baniso -3
1--17.33 Å20 Å27.32 Å2
2--56.27 Å20 Å2
3----38.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.69 Å0.66 Å
Luzzati d res low-5 Å
Luzzati sigma a1.16 Å1.26 Å
Refinement stepCycle: LAST / Resolution: 3.5→49.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16319 0 0 0 16319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 3.5→3.72 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 396 5 %
Rwork0.455 7571 -
obs--92.4 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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