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- PDB-3h1z: Molecular basis for the association of PIPKIgamma -p90 with the c... -

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Basic information

Entry
Database: PDB / ID: 3h1z
TitleMolecular basis for the association of PIPKIgamma -p90 with the clathrin adaptor AP-2
Components
  • AP-2 complex subunit beta-1
  • Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma
KeywordsENDOCYTOSIS / phosphatidylinositol 4 / 5-bisphosphate / clathrin / adaptor complex AP-2 / Alternative splicing / Cell membrane / Coated pit / Membrane / Phosphoprotein / Disease mutation / Kinase / Transferase
Function / homology
Function and homology information


AP-type membrane coat adaptor complex / 1-phosphatidylinositol-4-phosphate 5-kinase / postsynaptic endocytic zone / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / 1-phosphatidylinositol-4-phosphate 5-kinase activity / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 ...AP-type membrane coat adaptor complex / 1-phosphatidylinositol-4-phosphate 5-kinase / postsynaptic endocytic zone / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / 1-phosphatidylinositol-4-phosphate 5-kinase activity / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / clathrin coat / extrinsic component of presynaptic endocytic zone membrane / cardiac septum development / MHC class II antigen presentation / uropod / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / clathrin coat assembly / phosphatidylinositol kinase activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / membrane organization / clathrin-dependent endocytosis / coronary vasculature development / adherens junction assembly / positive regulation of protein localization to membrane / phosphatidylinositol biosynthetic process / neurotransmitter receptor internalization / aorta development / ventricular septum development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / clathrin binding / Trafficking of GluR2-containing AMPA receptors / Synthesis of PIPs at the plasma membrane / synaptic vesicle exocytosis / phosphatidylinositol phosphate biosynthetic process / positive regulation of endocytosis / phagocytic cup / synaptic vesicle endocytosis / phagocytosis / vesicle-mediated transport / neutrophil chemotaxis / kidney development / adherens junction / intracellular protein transport / cell-cell adhesion / ruffle membrane / synaptic vesicle / heart development / Clathrin-mediated endocytosis / presynapse / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / actin cytoskeleton organization / endosome membrane / focal adhesion / glutamatergic synapse / synapse / protein-containing complex binding / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Immunoglobulin-like - #1150 / 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 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain ...Immunoglobulin-like - #1150 / 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 / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / 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 / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TATA-Binding Protein / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Phosphatidylinositol 4-phosphate 5-kinase type-1 gamma / AP-2 complex subunit beta
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsVahedi-Faridi, A. / Kahlfeldt, N. / Schaefer, J.G. / Krainer, G. / Keller, S. / Saenger, W. / Krauss, M. / 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 14, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: AP-2 complex subunit beta-1
P: Phosphatidylinositol-4-phosphate 5-kinase type-1 gamma


Theoretical massNumber of molelcules
Total (without water)31,1462
Polymers31,1462
Non-polymers00
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-8 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.561, 83.469, 91.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AP-2 complex subunit beta-1 / Adapter-related protein complex 2 beta-1 subunit / Beta2-adaptin / Beta-adaptin / Plasma membrane ...Adapter-related protein complex 2 beta-1 subunit / Beta2-adaptin / Beta-adaptin / Plasma membrane adaptor HA2/AP2 adaptin beta subunit / Clathrin assembly protein complex 2 beta large chain / AP105B


Mass: 29246.605 Da / Num. of mol.: 1 / Fragment: UNP residues 701-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2b1, Clapb1 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (de3) / References: UniProt: P62944
#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: 1899.066 Da / Num. of mol.: 1 / Fragment: UNP residues 639-653 / Source method: obtained synthetically / Details: Synthetic peptide
References: UniProt: O60331, 1-phosphatidylinositol-4-phosphate 5-kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.31 Å3/Da / Density % sol: 46.64 % / Mosaicity: 0.843 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG8000, 100mM HEPES, pH7.5, 4mM DTT, 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: Apr 12, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 24788 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Χ2: 0.716 / Net I/σ(I): 20.383
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.83-1.93.60.46122560.60688.1
1.9-1.974.10.30523160.59189.4
1.97-2.064.50.20623230.60591.1
2.06-2.174.70.1723750.64292.3
2.17-2.314.70.14124380.63393.9
2.31-2.484.70.1225030.67496.1
2.48-2.734.70.09225580.69398.5
2.73-3.134.70.05926290.75899.6
3.13-3.944.80.03726440.89499.7
3.94-504.60.02827460.94297.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G30

2g30


Resolution: 1.83→34.25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.822 / SU B: 3.182 / SU ML: 0.099 / SU R Cruickshank DPI: 0.145 / SU Rfree: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1258 5.1 %RANDOM
Rwork0.193 ---
obs0.196 24729 94.48 %-
all-24788 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.9 Å2 / Biso mean: 23.699 Å2 / Biso min: 4.25 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å20 Å2
2--2.37 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.83→34.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2017 0 0 253 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222060
X-RAY DIFFRACTIONr_angle_refined_deg1.6181.9582808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.66925.62596
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45315355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.524155
X-RAY DIFFRACTIONr_chiral_restr0.2020.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021566
X-RAY DIFFRACTIONr_nbd_refined0.220.2874
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.223
X-RAY DIFFRACTIONr_mcbond_it1.1631.51292
X-RAY DIFFRACTIONr_mcangle_it1.95122050
X-RAY DIFFRACTIONr_scbond_it2.863884
X-RAY DIFFRACTIONr_scangle_it4.3654.5755
LS refinement shellResolution: 1.83→1.878 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.482 70 -
Rwork0.299 1578 -
all-1648 -
obs--85.74 %

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