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- PDB-1bxx: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1bxx
TitleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH TGN38 INTERNALIZATION PEPTIDE DYQRLN
Components
  • PROTEIN (AP50)
  • PROTEIN (TGN38 PEPTIDE)
KeywordsENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ADAPTOR / PEPTIDE COMPLEX / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex ...Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / positive regulation of synaptic vesicle endocytosis / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / low-density lipoprotein particle receptor binding / positive regulation of receptor internalization / Trafficking of GluR2-containing AMPA receptors / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / clathrin-coated pit / intracellular protein transport / terminal bouton / receptor internalization / disordered domain specific binding / synaptic vesicle / cytoplasmic vesicle / protein-containing complex assembly / postsynapse / transmembrane transporter binding / lipid binding / glutamatergic synapse / synapse / plasma membrane
Similarity search - Function
Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit ...Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Adaptor complexes medium subunit family / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Mu homology domain / Mu homology domain (MHD) profile. / Longin-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOwen, D.J. / Evans, P.R.
CitationJournal: Science / Year: 1998
Title: A structural explanation for the recognition of tyrosine-based endocytotic signals.
Authors: Owen, D.J. / Evans, P.R.
History
DepositionOct 8, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / pdbx_entity_src_syn / Item: _entity.src_method
Revision 1.4Aug 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (AP50)
P: PROTEIN (TGN38 PEPTIDE)


Theoretical massNumber of molelcules
Total (without water)33,5672
Polymers33,5672
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-5 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.260, 125.260, 73.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

#1: Protein PROTEIN (AP50) / MU2 ADAPTIN


Mass: 32758.363 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE FIRST SEVEN RESIDUES OF THE POLYMER MAKE UP A HIS-TAG
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PMW172H6 / Species (production host): Escherichia coli / Gene (production host): AP50 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P84092
#2: Protein/peptide PROTEIN (TGN38 PEPTIDE)


Mass: 808.860 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: HEXAPEPTIDE INTERNALISATION SIGNAL MOTIF FROM TGN38 DYQRLN
Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 4.98 Å3/Da / Density % sol: 75.3 % / Description: ISOMORPHOUS TO 1BW8
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: HANGING DROP, 2.2M NACL, 0.4M NA/K PHOSPHATE, 10MM DTT 0.1M MES PH 7.1, 15% GLYCEROL, 16DEGREES, MOLAR RATIO OF PEPTIDE TO PROTEIN 3:1, vapor diffusion - hanging drop, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / PH range low: 7.1 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.2 M1reservoirNaCl
20.4 MNa/K phosphate1reservoir
310 mMdithiothreitol1reservoir
415 %(v/v)glycerol1reservoir
50.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.877
DetectorType: ADSC / Detector: CCD / Date: Sep 12, 1998 / Details: MIRROR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.877 Å / Relative weight: 1
ReflectionResolution: 2.7→22 Å / Num. obs: 18413 / % possible obs: 99.8 % / Observed criterion σ(I): 4 / Redundancy: 15.8 % / Biso Wilson estimate: 78 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 23.5
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.9999999 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.99999 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BW8

1bw8


Resolution: 2.7→22 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.32
RfactorNum. reflection% reflectionSelection details
Rfree0.325 801 4.3 %RANDOM
Rwork0.263 ---
obs0.282 18413 98.4 %-
Displacement parametersBiso mean: 78 Å2
Refinement stepCycle: LAST / Resolution: 2.7→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2093 0 0 49 2142
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.040.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.82
X-RAY DIFFRACTIONp_mcangle_it3.14
X-RAY DIFFRACTIONp_scbond_it3.84
X-RAY DIFFRACTIONp_scangle_it5.35
X-RAY DIFFRACTIONp_plane_restr0.00250.01
X-RAY DIFFRACTIONp_chiral_restr0.1220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1980.3
X-RAY DIFFRACTIONp_multtor_nbd0.2520.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1890.3
X-RAY DIFFRACTIONp_planar_tor1.77
X-RAY DIFFRACTIONp_staggered_tor17.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor24.120
X-RAY DIFFRACTIONp_special_tor

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