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- PDB-1qtp: CRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE -

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Basic information

Entry
Database: PDB / ID: 1qtp
TitleCRYSTAL STRUCTURE OF THE AP-2 CLATHRIN ADAPTOR ALPHA-APPENDAGE
ComponentsAP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT (ALPHA-ADAPTIN C)
KeywordsMEMBRANE PROTEIN / FOUR-WAVELENGTH MAD / SELENOMETHIONINE
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 / protein serine/threonine kinase binding / regulation of hematopoietic stem cell differentiation / 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 / Resolution: 1.6 Å
AuthorsTraub, L.M. / Downs, M.A. / Westrich, J.L. / Fremont, D.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of the alpha appendage of AP-2 reveals a recruitment platform for clathrin-coat assembly.
Authors: Traub, L.M. / Downs, M.A. / Westrich, J.L. / Fremont, D.H.
History
DepositionJun 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-2 CLATHRIN ADAPTOR ALPHA SUBUNIT (ALPHA-ADAPTIN C)


Theoretical massNumber of molelcules
Total (without water)28,0161
Polymers28,0161
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.700, 40.730, 41.840
Angle α, β, γ (deg.)99.68, 95.81, 113.60
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 28016.254 Da / Num. of mol.: 1 / Fragment: C-TERMINAL APPENDAGE (EAR) RESIDUES 701-938 / Mutation: SELENOMETHIONINE SUBSTITUTED PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: MUS MUSCULUS / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL4 / References: UniProt: P17427
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.5 M MAGNESIUM SULFATE, 100 MM MES, 10MM SPERMINE TETRA-HCL, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.5 Mmagnesium sulfate1reservoir
2100 mMMES1reservoir
39 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 19-ID11.07813
SYNCHROTRONAPS 19-ID20.97956
SYNCHROTRONAPS 19-ID30.97945
SYNCHROTRONAPS 19-ID40.94645
Detector
TypeIDDetectorDate
CUSTOM-MADE1CCDDec 5, 1998
2
3
4
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
3SINGLE WAVELENGTHMx-ray1
4SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.078131
20.979561
30.979451
40.946451
ReflectionResolution: 1.6→100 Å / Num. all: 57749 / Num. obs: 57749 / % possible obs: 95.8 % / Redundancy: 2.58 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.1
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.286 / % possible all: 94.8
Reflection
*PLUS
Num. measured all: 149455
Reflection shell
*PLUS
% possible obs: 94.8 % / Mean I/σ(I) obs: 7.3

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Processing

Software
NameClassification
SHARPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1487 5.1 %RANDOM 5%
Rwork0.168 ---
obs0.168 29053 97.1 %-
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0.05 Å2-0.08 Å2
2---0.1 Å20.02 Å2
3----0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 0 266 2223
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.26
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.411.5
X-RAY DIFFRACTIONx_mcangle_it2.092
X-RAY DIFFRACTIONx_scbond_it2.482
X-RAY DIFFRACTIONx_scangle_it3.832.5
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.278 155 5.4 %
Rwork0.262 2695 -
obs--95.7 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.26

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