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- PDB-1b9k: ALPHA-ADAPTIN APPENDAGE DOMAIN, FROM CLATHRIN ADAPTOR AP2 -

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Basic information

Entry
Database: PDB / ID: 1b9k
TitleALPHA-ADAPTIN APPENDAGE DOMAIN, FROM CLATHRIN ADAPTOR AP2
ComponentsPROTEIN (ALPHA-ADAPTIN APPENDAGE DOMAIN)
KeywordsENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ADAPTOR / 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 / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / regulation of hematopoietic stem cell differentiation / protein serine/threonine kinase binding / vesicle-mediated transport / Neutrophil degranulation / phosphatidylinositol binding / secretory granule / intracellular protein transport / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / synaptic vesicle / cytoplasmic vesicle / postsynapse / protein domain specific binding / protein-containing complex binding / protein kinase binding
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 / 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 ...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 / 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 / TATA-Binding Protein / TBP domain superfamily / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsOwen, D.J. / Evans, P.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: A structural explanation for the binding of multiple ligands by the alpha-adaptin appendage domain.
Authors: Owen, D.J. / Vallis, Y. / Noble, M.E. / Hunter, J.B. / Dafforn, T.R. / Evans, P.R. / McMahon, H.T.
History
DepositionFeb 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jul 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (ALPHA-ADAPTIN APPENDAGE DOMAIN)


Theoretical massNumber of molelcules
Total (without water)27,0171
Polymers27,0171
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.860, 40.870, 42.470
Angle α, β, γ (deg.)99.40, 95.29, 113.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PROTEIN (ALPHA-ADAPTIN APPENDAGE DOMAIN)


Mass: 27016.768 Da / Num. of mol.: 1 / Fragment: APPENDAGE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX 4T2 / Cellular location (production host): CYTOPLASM / Gene (production host): ALPHA-ADAPTIN C / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P17427
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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 %
Crystal growpH: 6
Details: 20% PEG 4000, 10% ISOPROPANOL, 100MM NA CITRATE PH 6.0, 10MM DTT, 6MG/ML PROTEIN
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG40001reservoir
210 %isopropanol1reservoir
3100 mMsodium citrate1reservoir
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1997
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→15.55 Å / Num. obs: 51805 / % possible obs: 97 % / Observed criterion σ(I): 6 / Redundancy: 2.8 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 6.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.235 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 16 Å / % possible obs: 96.9 %
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.295

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Processing

Software
NameVersionClassification
SHARPSOLOMONphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLOMONphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→15.55 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1444 8 %RANDOM
Rwork0.163 ---
obs0.172 18198 97 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å20.14 Å20.04 Å2
2---0.6 Å20.13 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 0 302 2177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.53
X-RAY DIFFRACTIONp_mcangle_it3.25
X-RAY DIFFRACTIONp_scbond_it4.44
X-RAY DIFFRACTIONp_scangle_it66
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1230.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1090.3
X-RAY DIFFRACTIONp_planar_tor4.47
X-RAY DIFFRACTIONp_staggered_tor1315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor2120
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.169 / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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