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- PDB-9f8t: Clathrin terminal domain complexed with C-terminus of AAK1L -

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Basic information

Entry
Database: PDB / ID: 9f8t
TitleClathrin terminal domain complexed with C-terminus of AAK1L
Components
  • AP2-associated protein kinase 1
  • Clathrin heavy chain 1
KeywordsENDOCYTOSIS / membrane traffic / kinase
Function / homology
Function and homology information


Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / regulation of clathrin-dependent endocytosis / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle ...Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / regulation of clathrin-dependent endocytosis / Golgi Associated Vesicle Biogenesis / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / MHC class II antigen presentation / VLDLR internalisation and degradation / AP-2 adaptor complex binding / clathrin coat of coated pit / clathrin coat assembly / clathrin coat disassembly / Cargo recognition for clathrin-mediated endocytosis / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / membrane organization / arrestin family protein binding / Notch binding / clathrin-coated vesicle / presynaptic endocytosis / positive regulation of Notch signaling pathway / cell leading edge / clathrin-coated pit / receptor-mediated endocytosis / intracellular protein transport / terminal bouton / autophagy / spindle / disordered domain specific binding / melanosome / Cargo recognition for clathrin-mediated endocytosis / mitotic cell cycle / presynapse / regulation of protein localization / Clathrin-mediated endocytosis / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / non-specific serine/threonine protein kinase / protein stabilization / protein phosphorylation / protein domain specific binding / cell division / protein serine kinase activity / protein serine/threonine kinase activity / intracellular membrane-bounded organelle / structural molecule activity / mitochondrion / ATP binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / : / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS ...: / : / Clathrin, heavy chain, linker, core motif / Clathrin heavy chain, N-terminal / Clathrin, heavy chain / Clathrin, heavy chain, propeller repeat / Clathrin propeller repeat / Clathrin, heavy-chain linker / Clathrin-H-link / Region in Clathrin and VPS / Clathrin heavy chain repeat homology / Clathrin, heavy chain/VPS, 7-fold repeat / Clathrin heavy-chain (CHCR) repeat profile. / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Clathrin heavy chain 1 / AP2-associated protein kinase 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.711 Å
AuthorsWrobel, A.G. / Owen, D.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust097040/Z/11/Z United Kingdom
Wellcome Trust090909/Z/09/Z United Kingdom
CitationJournal: To Be Published
Title: Clathrin terminal domain complexed with C-terminus of AAK1L
Authors: Wrobel, A.G. / Owen, D.J. / Kadlecova, Z.
History
DepositionMay 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clathrin heavy chain 1
D: AP2-associated protein kinase 1
E: AP2-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)41,8283
Polymers41,8283
Non-polymers00
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Unstructured C-terminus of AAK1L can likely bind either of the two sites on the clathrin terminal domain: the clathrin box or the arrestin box
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-12 kcal/mol
Surface area16920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.539, 130.860, 77.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-645-

HOH

31A-724-

HOH

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Components

#1: Antibody Clathrin heavy chain 1


Mass: 40396.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CLTC / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: P49951
#2: Protein/peptide AP2-associated protein kinase 1 / Adaptor-associated kinase 1


Mass: 715.793 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Peptide derived from the C-terminus of the long isoform of AAK1 (AAK1L)
Source: (synth.) Homo sapiens (human)
References: UniProt: Q2M2I8, non-specific serine/threonine protein kinase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% PEG 3,350; 100 mM Bis-Tris propane, pH 6.0; 200 mM sodium citrate; 10 mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.71→28.3 Å / Num. obs: 56178 / % possible obs: 95.47 % / Redundancy: 1.87 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.0686 / Rpim(I) all: 0.0686 / Rrim(I) all: 0.097 / Net I/σ(I): 4.83
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5147 / CC1/2: 0.603 / CC star: 0.867 / Rpim(I) all: 0.452 / Rrim(I) all: 0.64 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
MOSFLM7.2.1data reduction
Aimless0.3.11 : 19/08/14data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.711→28.264 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2092 2770 4.931 %
Rwork0.1723 53407 -
all0.174 --
obs-56177 95.473 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.466 Å20 Å2-0 Å2
2--0.588 Å20 Å2
3----1.054 Å2
Refinement stepCycle: LAST / Resolution: 1.711→28.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2933 0 0 384 3317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123046
X-RAY DIFFRACTIONr_bond_other_d0.0020.0162937
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.8054137
X-RAY DIFFRACTIONr_angle_other_deg0.9061.7586768
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2385384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.123513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24710540
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.73410138
X-RAY DIFFRACTIONr_chiral_restr0.0870.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023599
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02677
X-RAY DIFFRACTIONr_nbd_refined0.1990.2492
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.22767
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21491
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0930.21691
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2302
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.219
X-RAY DIFFRACTIONr_nbd_other0.1790.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2540.229
X-RAY DIFFRACTIONr_mcbond_it2.5382.3551527
X-RAY DIFFRACTIONr_mcbond_other2.5292.3541527
X-RAY DIFFRACTIONr_mcangle_it3.8374.2081914
X-RAY DIFFRACTIONr_mcangle_other3.8434.2111915
X-RAY DIFFRACTIONr_scbond_it3.8052.81519
X-RAY DIFFRACTIONr_scbond_other3.8042.8021520
X-RAY DIFFRACTIONr_scangle_it5.9624.9332223
X-RAY DIFFRACTIONr_scangle_other5.9614.9342224
X-RAY DIFFRACTIONr_lrange_it8.05127.3483415
X-RAY DIFFRACTIONr_lrange_other7.8425.4873299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.711-1.7550.3131910.29435340.29542820.9370.94186.99210.294
1.755-1.8030.2981830.26237460.26441660.9450.95594.31110.262
1.803-1.8550.2581720.23337310.23440800.9570.96595.66180.233
1.855-1.9120.2341810.22335940.22439480.9630.96895.6180.223
1.912-1.9750.2491660.19435460.19638710.9610.97595.89250.194
1.975-2.0430.2261790.18533810.18736970.9680.97796.29430.185
2.043-2.120.2191790.18432460.18636070.9740.97994.95430.184
2.12-2.2060.221710.17931390.18134400.970.98196.22090.179
2.206-2.3040.1861500.16830320.16933130.9770.98296.04590.168
2.304-2.4150.2191630.16729560.1732050.9720.98297.31670.167
2.415-2.5450.2261630.16227200.16630280.9690.98395.21140.162
2.545-2.6980.1881340.15625730.15728560.9770.98494.78290.156
2.698-2.8820.1961480.15624950.15927180.9770.98497.24060.156
2.882-3.1110.221120.16523900.16725370.9680.98298.62040.165
3.111-3.4030.1961180.15821610.1623390.9760.98597.43480.158
3.403-3.7980.2141060.16119820.16421320.9750.98597.93620.161
3.798-4.3730.172870.14317660.14418850.9810.98798.30240.143
4.373-5.3240.167720.14315060.14416330.9860.98896.6320.143
5.324-7.3990.191610.19111830.19112810.9820.98397.11160.191
7.399-28.2640.22340.1757260.1778050.9720.97894.40990.175

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