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- PDB-1kyd: AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW P... -

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Basic information

Entry
Database: PDB / ID: 1kyd
TitleAP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH EPSIN DPW PEPTIDE
Components
  • ALPHA-ADAPTIN C
  • EH domain-binding mitotic phosphoprotein
KeywordsENDOCYTOSIS/EXOCYTOSIS / PROTEIN-PEPTIDE COMPLEX / ENDOCYTOSIS / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


negative regulation of sprouting angiogenesis / clathrin vesicle coat / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Recycling pathway of L1 / AP-2 adaptor complex ...negative regulation of sprouting angiogenesis / clathrin vesicle coat / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / Recycling pathway of L1 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / membrane coat / Clathrin-mediated endocytosis / clathrin adaptor activity / clathrin-dependent endocytosis / MHC class II antigen presentation / regulation of hematopoietic stem cell differentiation / clathrin binding / molecular sequestering activity / synaptic vesicle endocytosis / embryonic organ development / vesicle-mediated transport / Notch signaling pathway / clathrin-coated pit / Neutrophil degranulation / secretory granule / intracellular protein transport / EGFR downregulation / female pregnancy / phospholipid binding / kinase binding / cytoplasmic side of plasma membrane / endocytosis / disordered domain specific binding / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / cytoplasmic vesicle / in utero embryonic development / postsynapse / endosome / protein domain specific binding / lipid binding / protein kinase binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Gamma-adaptin ear (GAE) domain / ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / ENTH domain / TATA-Binding Protein / : ...Gamma-adaptin ear (GAE) domain / ENTH domain / Epsin N-terminal homology (ENTH) domain / ENTH domain profile. / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / ENTH 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 / ENTH/VHS / Ubiquitin-interacting motif. / TATA-Binding Protein / TBP domain superfamily / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / Armadillo-like helical / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / AP-2 complex subunit alpha-2 / Epsin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-ADAPTIN C
P: EH domain-binding mitotic phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6143
Polymers28,5182
Non-polymers961
Water3,243180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.780, 71.880, 41.670
Angle α, β, γ (deg.)90.00, 99.97, 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 EH domain-binding mitotic phosphoprotein / EPSIN 1


Mass: 689.737 Da / Num. of mol.: 1 / Fragment: RESIDUES 341-345 / Mutation: T345K / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence used (SPDWK) is a single mutation to the naturally occuring sequence from Human Epsin (SPDWT)
References: GenBank: 5051636, UniProt: Q9Y6I3*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.11 Å3/Da / Density % sol: 41.66 %
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: Nov 26, 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: 2→50 Å / Num. all: 16055 / Num. obs: 16055 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.0076 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.7 / Rsym value: 0.285 / % possible all: 84.1
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 59931 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 84.1 % / Rmerge(I) obs: 0.285

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Processing

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

1qts


Resolution: 2→19.73 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1530022.23 / Data cutoff high rms absF: 1530022.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 715 5 %RANDOM
Rwork0.178 ---
all-15157 --
obs-14442 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.8004 Å2 / ksol: 0.4041 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.35 Å20 Å22.51 Å2
2--6.79 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2002 0 5 180 2187
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 98 4.6 %
Rwork0.201 2032 -
obs--79.6 %
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
Rfactor obs: 0.178 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.06
LS refinement shell
*PLUS
Rfactor Rfree: 0.271 / Rfactor Rwork: 0.201 / Rfactor obs: 0.201

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