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- PDB-2bp5: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -

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Basic information

Entry
Database: PDB / ID: 2bp5
TitleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH NON-CANONICAL INTERNALIZATION PEPTIDE VEDYEQGLSG
Components
  • CLATHRIN COAT ASSEMBLY PROTEIN AP50
  • P2X PURINOCEPTOR 4
KeywordsENDOCYTOSIS / ADAPTOR / COATED PITS / ENDOCYTOSIS-EXOCYTOSIS / ENDOCYTOSIS/EXOCYTOSIS / PEPTIDE COMPLEX
Function / homology
Function and homology information


Platelet homeostasis / sensory perception of touch / Elevation of cytosolic Ca2+ levels / 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 / positive regulation of microglial cell migration ...Platelet homeostasis / sensory perception of touch / Elevation of cytosolic Ca2+ levels / 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 / positive regulation of microglial cell migration / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / purinergic nucleotide receptor signaling pathway / MHC class II antigen presentation / extracellularly ATP-gated monoatomic cation channel activity / purinergic nucleotide receptor activity / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / ligand-gated calcium channel activity / Recycling pathway of L1 / negative regulation of cardiac muscle hypertrophy / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / regulation of chemotaxis / response to fluid shear stress / vesicle budding from membrane / clathrin-dependent endocytosis / ATP-gated ion channel activity / signal sequence binding / inorganic cation transmembrane transport / positive regulation of endothelial cell chemotaxis / cellular response to zinc ion / relaxation of cardiac muscle / low-density lipoprotein particle receptor binding / cellular response to ATP / response to ATP / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / behavioral response to pain / positive regulation of receptor internalization / synaptic vesicle endocytosis / membrane depolarization / positive regulation of blood vessel endothelial cell migration / response to axon injury / regulation of cardiac muscle contraction / negative regulation of protein localization to plasma membrane / neuronal action potential / regulation of sodium ion transport / clathrin-coated pit / sensory perception of pain / nitric oxide biosynthetic process / positive regulation of calcium-mediated signaling / response to ischemia / excitatory postsynaptic potential / intracellular protein transport / apoptotic signaling pathway / postsynaptic density membrane / terminal bouton / calcium ion transmembrane transport / receptor internalization / regulation of blood pressure / calcium ion transport / disordered domain specific binding / vasodilation / cell junction / apical part of cell / synaptic vesicle / cell body / protein-containing complex assembly / cytoplasmic vesicle / monoatomic ion transmembrane transport / dendritic spine / transmembrane transporter binding / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / cadherin binding / copper ion binding / axon / signaling receptor binding / lysosomal membrane / neuronal cell body / synapse / lipid binding / dendrite / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / zinc ion binding / ATP binding / identical protein binding / membrane / plasma membrane
Similarity search - Function
P2X4 purinoceptor / Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Clathrin adaptor complexes medium chain signature 1. ...P2X4 purinoceptor / Mu homology domain, subdomain B / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / : / ATP P2X receptors signature. / ATP P2X receptor / P2X purinoreceptor / P2X purinoreceptor extracellular domain superfamily / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / AP complex, mu/sigma subunit / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / 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
P2X purinoceptor 4 / AP-2 complex subunit mu
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRoyle, S.J. / Evans, P.R. / Owen, D.J. / Murrell-Lagnado, R.D.
CitationJournal: J.Cell.Sci / Year: 2005
Title: Non-Canonical Yxxg-Phi Endocytic Motifs: Recognition by Ap2 and Preferential Utilization in P2X4 Receptors.
Authors: Royle, S.J. / Qureshi, O.S. / Bobanovic, L.K. / Evans, P.R. / Owen, D.J. / Murrell-Lagnado, R.D.
History
DepositionApr 18, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
M: CLATHRIN COAT ASSEMBLY PROTEIN AP50
P: P2X PURINOCEPTOR 4


Theoretical massNumber of molelcules
Total (without water)50,8232
Polymers50,8232
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)124.997, 124.997, 74.661
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11M-2012-

HOH

DetailsALTHOUGH CHAIN M IS A DOMAIN OF A LARGER PROTEINWHICH EXISTS IN ITS NATIVE STATE AS A TETRAMER, THISENTRY IS ANNOTATED AS A DIMER AS IT IS IN COMPLEXWITH A SMALL PEPTIDE (CHAIN P).

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Components

#1: Protein CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT ASSOCIATED PROTEIN AP50 / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / CLATHRIN ...CLATHRIN COAT ASSOCIATED PROTEIN AP50 / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN / AP-2 MU 2 CHAIN


Mass: 49726.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P84092
#2: Protein/peptide P2X PURINOCEPTOR 4 / ATP RECEPTOR / P2X4 / PURINERGIC RECEPTOR


Mass: 1096.103 Da / Num. of mol.: 1 / Fragment: RESIDUES 375-384 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: P51577
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: COMPONENT OF THE ADAPTOR COMPLEXES WHICH LINK CLATHRIN TO RECEPTORS IN COATED VESICLES. ...FUNCTION: COMPONENT OF THE ADAPTOR COMPLEXES WHICH LINK CLATHRIN TO RECEPTORS IN COATED VESICLES. CLATHRIN-ASSOCIATED PROTEIN COMPLEXES ARE BELIEVED TO INTERACT WITH THE CYTOPLASMIC TAILS OF MEMBRANE PROTEINS, LEADING TO THEIR SELECTION AND CONCENTRATION. AP50 IS A SUBUNIT OF THE PLASMA MEMBRANE ADAPTOR. THE COMPLEX BINDS POLYPHOSPHOINOSITIDE-CONTAINING LIPIDS.

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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: 2.8 Å3/Da / Density % sol: 60 % / Description: ISOMORPHOUS CRYSTAL TO 1BXX
Crystal growTemperature: 289 K / pH: 7.1
Details: 2.2M NACL, 0.4M NA/K PHOSPHATE PH 7.1, 10MM DTT, 0.1M MES, 15% GLYCEROL, 16 DEGREES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→23.6 Å / Num. obs: 16497 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 17.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 36
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 15.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0009refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXX

1bxx


Resolution: 2.8→105.41 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.915 / SU B: 9.807 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.305 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 825 5 %RANDOM
Rwork0.192 ---
obs0.195 15655 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 72.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20.09 Å20 Å2
2--0.19 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→105.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 0 69 2170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222142
X-RAY DIFFRACTIONr_bond_other_d0.0010.022026
X-RAY DIFFRACTIONr_angle_refined_deg1.9781.9812884
X-RAY DIFFRACTIONr_angle_other_deg0.90334719
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8515259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.97523.18288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.91915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0161517
X-RAY DIFFRACTIONr_chiral_restr0.1020.2320
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
X-RAY DIFFRACTIONr_nbd_refined0.2030.2360
X-RAY DIFFRACTIONr_nbd_other0.2060.21983
X-RAY DIFFRACTIONr_nbtor_refined0.190.2980
X-RAY DIFFRACTIONr_nbtor_other0.0960.21493
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5381.51622
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.84822135
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4853970
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.7944.5749
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.376 69
Rwork0.367 1147

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