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- PDB-3h85: Molecular basis for the association of PIPKI gamma-p90 with the c... -

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Basic information

Entry
Database: PDB / ID: 3h85
TitleMolecular basis for the association of PIPKI gamma-p90 with the clathrin adaptor AP-2
Components
  • AP-2 complex subunit mu-1
  • Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma
KeywordsENDOCYTOSIS / phosphatidylinositol 4 / 5-bisphosphate / clathrin / adaptor complex AP-2 / Cell membrane / Coated pit / Lipid-binding / Membrane / Phosphoprotein / Disease mutation / Kinase / Transferase
Function / homology
Function and homology information


1-phosphatidylinositol-4-phosphate 5-kinase / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / 1-phosphatidylinositol-4-phosphate 5-kinase activity / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane ...1-phosphatidylinositol-4-phosphate 5-kinase / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / 1-phosphatidylinositol-4-phosphate 5-kinase activity / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / uropod / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / phosphatidylinositol kinase activity / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / vesicle budding from membrane / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / clathrin-dependent endocytosis / adherens junction assembly / membrane organization / phosphatidylinositol biosynthetic process / signal sequence binding / negative regulation of protein localization to plasma membrane / low-density lipoprotein particle receptor binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic vesicle exocytosis / Trafficking of GluR2-containing AMPA receptors / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / positive regulation of receptor internalization / phagocytic cup / synaptic vesicle endocytosis / phagocytosis / clathrin-coated pit / neutrophil chemotaxis / adherens junction / intracellular protein transport / terminal bouton / receptor internalization / ruffle membrane / cell-cell adhesion / disordered domain specific binding / presynapse / Clathrin-mediated endocytosis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / actin cytoskeleton organization / postsynapse / protein-containing complex assembly / transmembrane transporter binding / endosome membrane / phosphorylation / focal adhesion / glutamatergic synapse / lipid binding / synapse / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Mu homology domain, subdomain B / Phosphatidylinositol-4-phosphate 5-kinase / : / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal ...Mu homology domain, subdomain B / Phosphatidylinositol-4-phosphate 5-kinase / : / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases / 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. / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsVahedi-Faridi, A. / Kahlfeldt, N. / Schaefer, J.G. / Haucke, V.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Molecular basis for association of PIPKI gamma-p90 with clathrin adaptor AP-2.
Authors: Kahlfeldt, N. / Vahedi-Faridi, A. / Koo, S.J. / Schafer, J.G. / Krainer, G. / Keller, S. / Saenger, W. / Krauss, M. / Haucke, V.
History
DepositionApr 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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-1
P: Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1493
Polymers35,0902
Non-polymers591
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1150 Å2
ΔGint-8 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.301, 125.301, 74.546
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein AP-2 complex subunit mu-1 / Mu2-adaptin / AP-2 mu-2 chain / Plasma membrane adaptor AP-2 50 kDa protein / Clathrin assembly ...Mu2-adaptin / AP-2 mu-2 chain / Plasma membrane adaptor AP-2 50 kDa protein / Clathrin assembly protein complex 2 medium chain / Clathrin coat assembly protein AP50 / Clathrin coat-associated protein AP50


Mass: 34100.840 Da / Num. of mol.: 1 / Fragment: UNP residues 158-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (de3) / References: UniProt: P84092
#2: Protein/peptide Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma / Phosphatidylinositol-4-phosphate 5-kinase type I gamma / PtdIns(4)P-5-kinase gamma / PtdInsPKIgamma ...Phosphatidylinositol-4-phosphate 5-kinase type I gamma / PtdIns(4)P-5-kinase gamma / PtdInsPKIgamma / PIP5KIgamma


Mass: 989.105 Da / Num. of mol.: 1 / Fragment: UNP residues 646-653 / Source method: obtained synthetically / Details: Synthetic peptide
References: UniProt: O60331, 1-phosphatidylinositol-4-phosphate 5-kinase
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 4.81 Å3/Da / Density % sol: 74.45 % / Mosaicity: 0.585 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.4M sodium formate, 50mM NiCl, 0.1M Na-acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 20, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19090 / % possible obs: 92.6 % / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Χ2: 0.907 / Net I/σ(I): 15.965
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.691.80.48410030.81649
2.69-2.82.70.41716620.82281.5
2.8-2.933.30.30319900.82297
2.93-3.083.70.20120260.912100
3.08-3.283.80.1420620.977100
3.28-3.533.80.09920651.00299.9
3.53-3.883.80.07820440.92699.8
3.88-4.453.70.06320560.87399.6
4.45-5.63.60.06120680.91599.4
5.6-503.60.04521140.86699.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BW8

1bw8


Resolution: 2.6→41.01 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.269 / WRfactor Rwork: 0.245 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.771 / SU B: 9.632 / SU ML: 0.201 / SU R Cruickshank DPI: 0.295 / SU Rfree: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 792 4.2 %RANDOM
Rwork0.231 ---
obs0.233 19070 92.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.29 Å2 / Biso mean: 64.634 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.04 Å20 Å2
2---0.07 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.6→41.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2110 0 1 31 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222155
X-RAY DIFFRACTIONr_angle_refined_deg1.1511.9782902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9095257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12222.41487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95915414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3931519
X-RAY DIFFRACTIONr_chiral_restr0.0690.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211571
X-RAY DIFFRACTIONr_mcbond_it0.5531.51305
X-RAY DIFFRACTIONr_mcangle_it1.04722129
X-RAY DIFFRACTIONr_scbond_it1.2253850
X-RAY DIFFRACTIONr_scangle_it2.2514.5773
LS refinement shellResolution: 2.603→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.507 28 -
Rwork0.373 645 -
all-673 -
obs--44.16 %

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