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- PDB-6qh5: AP2 clathrin adaptor mu2T156-phosphorylated core in closed confor... -

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Basic information

Entry
Database: PDB / ID: 6qh5
TitleAP2 clathrin adaptor mu2T156-phosphorylated core in closed conformation
Components(AP-2 complex subunit ...) x 5
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS / PHOSPHORYLATION / CELL MEMBRANE
Function / homology
Function and homology information


secretory vesicle / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance ...secretory vesicle / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor complex / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / Recycling pathway of L1 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / neurotransmitter secretion / endolysosome membrane / aorta development / Neutrophil degranulation / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of receptor internalization / positive regulation of endocytosis / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / clathrin-coated pit / phosphatidylinositol binding / MHC class II antigen presentation / protein serine/threonine kinase binding / VLDLR internalisation and degradation / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / receptor internalization / kinase binding / cytoplasmic side of plasma membrane / terminal bouton / disordered domain specific binding / synaptic vesicle / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain ...Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Beta-Lactamase / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / AP-2 complex subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsWrobel, A.G. / Owen, D.J. / McCoy, A.J. / Evans, P.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust090909/Z/09/Z United Kingdom
Wellcome Trust097040/Z/11/Z United Kingdom
CitationJournal: Dev.Cell / Year: 2019
Title: Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation.
Authors: Wrobel, A.G. / Kadlecova, Z. / Kamenicky, J. / Yang, J.C. / Herrmann, T. / Kelly, B.T. / McCoy, A.J. / Evans, P.R. / Martin, S. / Muller, S. / Sroubek, F. / Neuhaus, D. / Honing, S. / Owen, D.J.
History
DepositionJan 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2Jan 24, 2024Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-2 complex subunit alpha
B: AP-2 complex subunit beta
N: AP-2 complex subunit mu
M: AP-2 complex subunit mu
S: AP-2 complex subunit sigma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,6156
Polymers255,9555
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20080 Å2
ΔGint-79 kcal/mol
Surface area70940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.037, 121.037, 257.671
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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AP-2 complex subunit ... , 5 types, 5 molecules ABNMS

#1: Protein AP-2 complex subunit alpha


Mass: 69656.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2a2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66HM2, UniProt: P18484*PLUS
#2: Protein AP-2 complex subunit beta / AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta ...AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta / Beta-2-adaptin / Beta-adaptin / Clathrin assembly protein complex 2 beta large chain / Plasma membrane adaptor HA2/AP2 adaptin beta subunit


Mass: 67091.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP2B1, ADTB2, CLAPB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63010
#3: 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: 51044.113 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
#4: 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: 51124.094 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
#5: Protein AP-2 complex subunit sigma / Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / ...Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / Clathrin assembly protein 2 sigma small chain / Clathrin coat assembly protein AP17 / Clathrin coat-associated protein AP17 / Plasma membrane adaptor AP-2 17 kDa protein / Sigma-adaptin 3b / Sigma2-adaptin


Mass: 17038.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2s1, Ap17, Claps2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62743

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Non-polymers , 1 types, 1 molecules

#6: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6

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Details

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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 1000; 100 mM Na+/K+ phosphate buffer (pH 7.2), 200 mM NaCl, and 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.56→60.52 Å / Num. obs: 71252 / % possible obs: 99.8 % / Redundancy: 17.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.32 / Rpim(I) all: 0.109 / Rrim(I) all: 0.339 / Net I/σ(I): 8.4
Reflection shellResolution: 2.56→2.62 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vgl

2vgl


Resolution: 2.56→60.52 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.775 / SU ML: 0.289 / Cross valid method: THROUGHOUT / ESU R: 0.612 / ESU R Free: 0.302 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25689 3551 5 %RANDOM
Rwork0.22453 ---
obs0.22614 67643 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 70.521 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20.21 Å20 Å2
2--0.43 Å20 Å2
3----1.39 Å2
Refinement stepCycle: 1 / Resolution: 2.56→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13707 0 36 0 13743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01914017
X-RAY DIFFRACTIONr_bond_other_d0.0030.0213807
X-RAY DIFFRACTIONr_angle_refined_deg1.7931.97518991
X-RAY DIFFRACTIONr_angle_other_deg1.098331730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9451716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97324.293629
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.862152578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8231593
X-RAY DIFFRACTIONr_chiral_restr0.1010.22207
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215594
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023115
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_it5.3976.9576875
X-RAY DIFFRACTIONr_mcbond_other5.3976.9586874
X-RAY DIFFRACTIONr_mcangle_it8.37410.4148588
X-RAY DIFFRACTIONr_mcangle_other8.37310.4148589
X-RAY DIFFRACTIONr_scbond_it4.9977.2327140
X-RAY DIFFRACTIONr_scbond_other4.9967.2327137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.97610.70910402
X-RAY DIFFRACTIONr_long_range_B_refined12.34582.23215984
X-RAY DIFFRACTIONr_long_range_B_other12.34582.23415985
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.558→2.624 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 218 -
Rwork0.369 5000 -
obs--99.87 %

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