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- PDB-2pr9: Mu2 adaptin subunit (AP50) of AP2 adaptor (second domain), comple... -

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Basic information

Entry
Database: PDB / ID: 2pr9
TitleMu2 adaptin subunit (AP50) of AP2 adaptor (second domain), complexed with GABAA receptor-gamma2 subunit-derived internalization peptide DEEYGYECL
Components
  • AP-2 complex subunit mu-1
  • GABA(A) receptor subunit gamma-2 peptide
KeywordsENDOCYTOSIS / adaptor / internalization peptide complex / inhibitory neurotransmitter receptor
Function / homology
Function and homology information


GABA receptor activation / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation ...GABA receptor activation / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / AP-2 adaptor complex / inhibitory synapse / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / GABA receptor complex / inhibitory extracellular ligand-gated monoatomic ion channel activity / Recycling pathway of L1 / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / vesicle budding from membrane / clathrin-dependent endocytosis / signal sequence binding / postsynaptic specialization membrane / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / negative regulation of protein localization to plasma membrane / chloride transport / low-density lipoprotein particle receptor binding / chloride channel activity / adult behavior / Trafficking of GluR2-containing AMPA receptors / chloride channel complex / positive regulation of receptor internalization / synaptic vesicle endocytosis / GABA-ergic synapse / regulation of postsynaptic membrane potential / clathrin-coated pit / chloride transmembrane transport / dendrite membrane / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / intracellular protein transport / cytoplasmic vesicle membrane / terminal bouton / receptor internalization / disordered domain specific binding / cytoplasmic vesicle / chemical synaptic transmission / postsynapse / protein-containing complex assembly / transmembrane transporter binding / neuron projection / axon / synapse / glutamatergic synapse / lipid binding / plasma membrane
Similarity search - Function
Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / 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 ...Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / 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 / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit gamma-2 / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsVahedi-Faridi, A. / Haucke, V. / Kittler, J.T. / Kukhtina, V. / Moss, S.J. / Saenger, W. / Chen, G.-J. / Tretter, V. / Smith, K. / Yan, Z. ...Vahedi-Faridi, A. / Haucke, V. / Kittler, J.T. / Kukhtina, V. / Moss, S.J. / Saenger, W. / Chen, G.-J. / Tretter, V. / Smith, K. / Yan, Z. / McAinsh, K. / Arancibia-Carcamo, L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Regulation of synaptic inhibition by phospho-dependent binding of the AP2 complex to a YECL motif in the GABAA receptor gamma2 subunit.
Authors: Kittler, J.T. / Chen, G. / Kukhtina, V. / Vahedi-Faridi, A. / Gu, Z. / Tretter, V. / Smith, K.R. / McAinsh, K. / Arancibia-Carcamo, I.L. / Saenger, W. / Haucke, V. / Yan, Z. / Moss, S.J.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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
Remark 300BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-2 complex subunit mu-1
P: GABA(A) receptor subunit gamma-2 peptide


Theoretical massNumber of molelcules
Total (without water)35,3362
Polymers35,3362
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-5.2 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.300, 126.300, 74.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein AP-2 complex subunit mu-1


Mass: 34100.840 Da / Num. of mol.: 1 / Fragment: second domain (residues 158-435)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2m1 / Plasmid: pET-28a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P84092
#2: Protein/peptide GABA(A) receptor subunit gamma-2 peptide


Mass: 1235.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in mouse and rat.
References: UniProt: P18508
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 4.86 Å3/Da / Density % sol: 74.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 2.0 M sodium formate, 0.1 M Na-acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.95373
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22817 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Biso Wilson estimate: 66.389 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.14
Reflection shellResolution: 2.5→2.75 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1 / Num. unique all: 3053 / % possible all: 68.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation3.18 Å9.97 Å
Translation3.18 Å9.97 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BW8

1bw8


Resolution: 2.51→9.97 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 15.237 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 913 4 %RANDOM
Rwork0.203 ---
obs0.204 22817 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.027 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0.49 Å20 Å2
2---0.98 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.51→9.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 0 59 2174
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0360.0222157
X-RAY DIFFRACTIONr_angle_refined_deg2.6411.9812905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.4335260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.85823.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16915409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5131517
X-RAY DIFFRACTIONr_chiral_restr0.1930.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021585
X-RAY DIFFRACTIONr_nbd_refined0.2410.2815
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21431
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.290
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3470.211
X-RAY DIFFRACTIONr_mcbond_it1.4221.51370
X-RAY DIFFRACTIONr_mcangle_it2.26422143
X-RAY DIFFRACTIONr_scbond_it3.6173934
X-RAY DIFFRACTIONr_scangle_it5.3734.5762
LS refinement shellResolution: 2.512→2.573 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.455 63 -
Rwork0.431 1504 -
obs-1567 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.48291.2208-2.55231.8875-0.03522.1263-0.28310.0438-0.5692-0.16670.0883-0.20080.2371-0.1060.1949-0.04710.0397-0.0645-0.11440.0668-0.1159-43.838240.619925.3328
241.338-12.4676-16.44330.32722.762521.4441-1.4882-3.13160.63072.80121.19680.8733-0.2527-0.75720.29140.0735-0.0263-0.01160.0299-0.06180.0273-32.244550.928527.7458
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA159 - 21923 - 83
21AA238 - 255102 - 119
31AA261 - 435125 - 299
42PB1 - 101 - 10

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