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- PDB-1kyu: AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF P... -

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Basic information

Entry
Database: PDB / ID: 1kyu
TitleAP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPS15 DPF PEPTIDE
Components
  • ALPHA-ADAPTIN C
  • EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15
KeywordsENDOCYTOSIS/EXOCYTOSIS / PROTEIN-PEPTIDE COMPLEX / ENDOCYTOSIS / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


Negative regulation of MET activity / EGFR downregulation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / ubiquitin-dependent endocytosis / VLDLR internalisation and degradation / Recycling pathway of L1 ...Negative regulation of MET activity / EGFR downregulation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / ubiquitin-dependent endocytosis / VLDLR internalisation and degradation / Recycling pathway of L1 / Golgi to endosome transport / clathrin coat of coated pit / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / clathrin adaptor activity / clathrin-dependent endocytosis / MHC class II antigen presentation / endocytic recycling / regulation of hematopoietic stem cell differentiation / clathrin-coated vesicle / aggresome / ciliary membrane / positive regulation of receptor recycling / polyubiquitin modification-dependent protein binding / synaptic vesicle endocytosis / vesicle-mediated transport / receptor-mediated endocytosis of virus by host cell / clathrin-coated pit / Neutrophil degranulation / basal plasma membrane / secretory granule / ubiquitin binding / intracellular protein transport / SH3 domain binding / kinase binding / cytoplasmic side of plasma membrane / disordered domain specific binding / presynapse / regulation of cell population proliferation / regulation of protein localization / cytoplasmic vesicle / early endosome membrane / postsynapse / apical plasma membrane / protein domain specific binding / calcium ion binding / lipid binding / protein kinase binding / glutamatergic synapse / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Gamma-adaptin ear (GAE) domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / EH domain / EH domain profile. / Eps15 homology domain / EH domain / TATA-Binding Protein / : ...Gamma-adaptin ear (GAE) domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / EH domain / EH domain profile. / Eps15 homology domain / EH domain / TATA-Binding Protein / : / 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 / Ubiquitin-interacting motif. / TATA-Binding Protein / TBP domain superfamily / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Armadillo-like helical / EF-hand domain pair / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AP-2 complex subunit alpha-2 / Epidermal growth factor receptor substrate 15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrett, T.J. / Traub, L.M. / Fremont, D.H.
CitationJournal: Structure / Year: 2002
Title: Accessory protein recruitment motifs in clathrin-mediated endocytosis.
Authors: Brett, T.J. / Traub, L.M. / Fremont, D.H.
History
DepositionFeb 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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: ALPHA-ADAPTIN C
P: EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15


Theoretical massNumber of molelcules
Total (without water)28,4792
Polymers28,4792
Non-polymers00
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.670, 40.750, 41.890
Angle α, β, γ (deg.)99.67, 99.95, 113.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ALPHA-ADAPTIN C / AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT


Mass: 27828.676 Da / Num. of mol.: 1 / Fragment: C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL4 / References: UniProt: P17427
#2: Protein/peptide EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15 / PROTEIN EPS15 / AF-1P PROTEIN


Mass: 650.701 Da / Num. of mol.: 1 / Fragment: RESIDUES 628-632 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is a naturally occuring sequence in EPS15 (MOUSE)
References: UniProt: P42567
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.02 Å3/Da / Density % sol: 39.21 %
Crystal grow
*PLUS
pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein/peptide solution1drop
21.36-1.49 Mammonium sulfate1reservoir
385-93 mMHEPES1reservoirpH6.8
48.5-9.3 %dioxane1reservoir
50-5 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 28, 2000 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 20976 / Num. obs: 20976 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.5 Å2 / Rsym value: 0.052 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.382 / % possible all: 89.3
Reflection
*PLUS
Num. measured all: 86516 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 89.3 % / Rmerge(I) obs: 0.382

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QTP

1qtp


Resolution: 1.8→19.96 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 1127447.1 / Data cutoff high rms absF: 1127447.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 894 4.8 %RANDOM
Rwork0.187 ---
all0.188 20976 --
obs-18506 87.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.4235 Å2 / ksol: 0.390539 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--10.36 Å21.12 Å24.7 Å2
2--5.15 Å21.45 Å2
3---5.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 0 197 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it1.762
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.082.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 140 5.3 %
Rwork0.293 2486 -
obs--74.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.PARAM
X-RAY DIFFRACTION3ION.PARAMION.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.188 / Rfactor obs: 0.187 / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.377 / Rfactor Rwork: 0.293 / Rfactor obs: 0.293

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