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

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Basic information

Entry
Database: PDB / ID: 1kyf
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


Degradation of CDH1 / Negative regulation of MET activity / EGFR downregulation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Retrograde neurotrophin signalling / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / Recycling pathway of L1 ...Degradation of CDH1 / Negative regulation of MET activity / EGFR downregulation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Retrograde neurotrophin signalling / Trafficking of GluR2-containing AMPA receptors / 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-cargo adaptor activity / clathrin-dependent endocytosis / MHC class II antigen presentation / endocytic recycling / clathrin-coated vesicle / regulation of hematopoietic stem cell differentiation / aggresome / endosomal transport / ubiquitin-dependent endocytosis / 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 / Neutrophil degranulation / clathrin-coated pit / basal plasma membrane / secretory granule / ubiquitin binding / intracellular protein transport / SH3 domain binding / cytoplasmic side of plasma membrane / kinase binding / endocytosis / disordered domain specific binding / regulation of cell population proliferation / regulation of protein localization / presynapse / cytoplasmic vesicle / early endosome membrane / protein-macromolecule adaptor activity / early endosome / apical plasma membrane / postsynapse / protein domain specific binding / calcium ion binding / synapse / symbiont entry into host cell / lipid binding / protein kinase binding / glutamatergic synapse / identical protein binding / plasma membrane / cytoplasm / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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 4, 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 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.620, 72.820, 41.860
Angle α, β, γ (deg.)90.00, 99.95, 90.00
Int Tables number4
Space group name H-MP1211

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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. It is naturally occuring sequence in Mus musculus (mouse) EPS15
References: UniProt: P42567
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 1.83 Å3/Da / Density % sol: 32.6 %
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: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. all: 67213 / Num. obs: 67213 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rsym value: 0.059 / Net I/σ(I): 15.6
Reflection shellResolution: 1.22→1.26 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.388 / % possible all: 84
Reflection
*PLUS
Num. measured all: 402957 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.388

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QTS

1qts


Resolution: 1.22→20 Å / Num. parameters: 19156 / Num. restraintsaints: 22808 / Cross valid method: FREE R / σ(F): 0 / σ(I): -3
StereochEM target val spec case: ANISOTROPIC REFINEMENT REDUCED FREE R
Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 3427 5.1 %RANDOM
Rwork0.1527 ---
all0.1543 67213 --
obs-67173 94.4 %-
Solvent computationSolvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-22
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 1897 / Occupancy sum non hydrogen: 2342
Refinement stepCycle: LAST / Resolution: 1.22→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 343 4239
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0301
X-RAY DIFFRACTIONs_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.058
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.1543 / Rfactor obs: 0.153 / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.03
X-RAY DIFFRACTIONs_chiral_restr0.065

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