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- PDB-1ky7: THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH AMPHIPH... -

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Basic information

Entry
Database: PDB / ID: 1ky7
TitleTHE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE IN COMPLEX WITH AMPHIPHYSIN FXDXF
Components
  • ALPHA-ADAPTIN C
  • AMPHIPHYSIN
KeywordsENDOCYTOSIS/EXOCYTOSIS / PROTEIN-PEPTIDE COMPLEX / ENDOCYTOSIS / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


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 ...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 / clathrin adaptor activity / Clathrin-mediated endocytosis / leading edge membrane / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / protein serine/threonine kinase binding / regulation of hematopoietic stem cell differentiation / synaptic vesicle endocytosis / vesicle-mediated transport / Neutrophil degranulation / phosphatidylinositol binding / secretory granule / intracellular protein transport / phospholipid binding / cytoplasmic side of plasma membrane / synaptic vesicle membrane / kinase binding / endocytosis / disordered domain specific binding / synaptic vesicle / actin cytoskeleton / Clathrin-mediated endocytosis / cytoplasmic vesicle / chemical synaptic transmission / postsynapse / protein domain specific binding / protein-containing complex binding / protein kinase binding / plasma membrane / cytosol
Similarity search - Function
Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Amphiphysin / Gamma-adaptin ear (GAE) domain / BAR domain / BAR domain profile. / BAR / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain ...Amphiphysin, isoform 1 / Amphiphysin I, SH3 domain / Amphiphysin / Gamma-adaptin ear (GAE) domain / BAR domain / BAR domain profile. / BAR / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / TATA-Binding Protein / BAR domain / 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 / AH/BAR domain superfamily / TATA-Binding Protein / TBP domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / Amphiphysin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 3, 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: AMPHIPHYSIN


Theoretical massNumber of molelcules
Total (without water)29,0592
Polymers29,0592
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.630, 73.690, 41.940
Angle α, β, γ (deg.)90.00, 99.74, 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 AMPHIPHYSIN /


Mass: 1230.278 Da / Num. of mol.: 1 / Fragment: RESIDUES 322-330 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is a naturally occuring sequence in Amphiphysin (Homo sapiens)
References: UniProt: P49418
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.13 Å3/Da / Density % sol: 42.21 %
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 1, 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: 2.15→50 Å / Num. all: 11788 / Num. obs: 11788 / % possible obs: 88.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.9 Å2 / Rsym value: 0.071 / Net I/σ(I): 13.8
Reflection shellResolution: 2.15→2.23 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.0404 / % possible all: 88.6
Reflection
*PLUS
Num. measured all: 41702 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 88.6 % / Rmerge(I) obs: 0.404

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Processing

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

1qts


Resolution: 2.15→19.9 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1457268.35 / Data cutoff high rms absF: 1457268.35 / 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
Rfree0.252 578 5.2 %RANDOM
Rwork0.187 ---
all0.188 11758 --
obs-11180 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0957 Å2 / ksol: 0.340561 e/Å3
Displacement parametersBiso mean: 29.3 Å2
Baniso -1Baniso -2Baniso -3
1--6.48 Å20 Å23.95 Å2
2--5.62 Å20 Å2
3---0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 0 162 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it2.262
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.366 74 6.1 %
Rwork0.292 1135 -
obs--55.2 %
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: 0.252 / 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_deg26.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.98
LS refinement shell
*PLUS
Rfactor Rfree: 0.366 / Rfactor Rwork: 0.292 / Rfactor obs: 0.292

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