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- PDB-5fpi: Mu2 adaptin subunit of the AP2 adaptor (C-terminal domain) comple... -

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Basic information

Entry
Database: PDB / ID: 5fpi
TitleMu2 adaptin subunit of the AP2 adaptor (C-terminal domain) complexed with Integrin alpha4 internalisation peptide QYKSILQE
Components
  • AP-2 COMPLEX SUBUNIT MU
  • INTEGRIN ALPHA-4 SUBUNIT
KeywordsENDOCYTOSIS / CLATHRIN ADAPTOR
Function / homology
Function and homology information


clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / negative regulation of protein homodimerization activity / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / cell-cell adhesion in response to extracellular stimulus / diapedesis / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / Gap junction degradation ...clathrin-dependent extracellular exosome endocytosis / immune response in gut-associated lymphoid tissue / negative regulation of protein homodimerization activity / cell-matrix adhesion involved in ameboidal cell migration / integrin alpha4-beta7 complex / cell-cell adhesion in response to extracellular stimulus / diapedesis / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / 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 / positive regulation of leukocyte tethering or rolling / AP-2 adaptor complex / regulation of vesicle size / postsynaptic neurotransmitter receptor internalization / axonogenesis involved in innervation / Recycling pathway of L1 / protein antigen binding / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / clathrin adaptor activity / vesicle budding from membrane / leukocyte tethering or rolling / clathrin-dependent endocytosis / positive regulation of endothelial cell apoptotic process / RUNX3 Regulates Immune Response and Cell Migration / signal sequence binding / negative regulation of protein localization to plasma membrane / heterotypic cell-cell adhesion / integrin complex / positive regulation of vascular endothelial cell proliferation / neuron projection extension / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / low-density lipoprotein particle receptor binding / endodermal cell differentiation / receptor clustering / cellular response to cytokine stimulus / Trafficking of GluR2-containing AMPA receptors / positive regulation of receptor internalization / fibronectin binding / synaptic vesicle endocytosis / positive regulation of T cell migration / Integrin cell surface interactions / coreceptor activity / clathrin-coated pit / cell adhesion molecule binding / B cell differentiation / substrate adhesion-dependent cell spreading / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / intracellular protein transport / terminal bouton / receptor internalization / cell-cell adhesion / cellular response to amyloid-beta / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / disordered domain specific binding / integrin binding / growth cone / cytoplasmic vesicle / postsynapse / protein-containing complex assembly / transmembrane transporter binding / Potential therapeutics for SARS / membrane => GO:0016020 / cell adhesion / external side of plasma membrane / focal adhesion / neuronal cell body / glutamatergic synapse / lipid binding / synapse / cell surface / extracellular exosome / membrane / metal ion binding / 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 / Clathrin adaptor complex small chain ...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. / : / Integrin alpha Ig-like domain 3 / Longin-like domain superfamily / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / Integrin domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Integrin alpha-4 / AP-2 complex subunit mu / Integrin alpha-4 subunit
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.77 Å
AuthorsOwen, D.J. / Evans, P.R. / Ivaska, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Selective Integrin Endocytosis is Driven by Alpha Chain:Ap2 Interactions
Authors: De Franceschi, N. / Arjonen, A. / Elkhatib, N. / Denessiouk, K. / Wrobel, A.G. / Wilson, T.A. / Pouwels, J. / Montagnac, G. / Owen, D.J. / Ivaska, J.
History
DepositionNov 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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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
B: INTEGRIN ALPHA-4 SUBUNIT


Theoretical massNumber of molelcules
Total (without water)52,0532
Polymers52,0532
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-3.6 kcal/mol
Surface area14760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.650, 125.650, 74.410
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 AP-2 COMPLEX SUBUNIT MU / AP-2 MU CHAIN / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT MU / ADAPTOR-RELATED PROTEIN COMPLEX 2 SUBUNIT ...AP-2 MU CHAIN / ADAPTOR PROTEIN COMPLEX AP-2 SUBUNIT MU / ADAPTOR-RELATED PROTEIN COMPLEX 2 SUBUNIT MU / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MU MEDIUM CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT-ASSOCIATED PROTEIN AP50 / HA2 50 KDA SUBUNIT / MU2- ADAPTIN / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN


Mass: 51044.113 Da / Num. of mol.: 1 / Fragment: INTERNALISATION SIGNAL BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PLASMID / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P84092
#2: Protein/peptide INTEGRIN ALPHA-4 SUBUNIT


Mass: 1009.134 Da / Num. of mol.: 1 / Fragment: INTERNALISATION SIGNAL PEPTIDE, RESIDUES 150-157 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q8IU71, UniProt: P13612*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.26 Å3/Da / Density % sol: 62.24 % / Description: NONE
Crystal growpH: 6.5
Details: 2.2M NACL, 0.4M NAKPHOSPHATE, 20% V/V GLYCEROL, 0.1M MES PH6.5, 5MM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.54182
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2015 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54182 Å / Relative weight: 1
ReflectionResolution: 2.75→74 Å / Num. obs: 17034 / % possible obs: 97.2 % / Observed criterion σ(I): -9.9 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.2
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.7 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BXX

1bxx


Resolution: 2.77→108.82 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.982 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 893 5.3 %RANDOM
Rwork0.17443 ---
obs0.17697 16115 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.116 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0.23 Å20 Å2
2---0.45 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.77→108.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 0 45 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192171
X-RAY DIFFRACTIONr_bond_other_d0.0020.022195
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9812918
X-RAY DIFFRACTIONr_angle_other_deg1.06135059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.415260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.07222.72788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.60515427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8161519
X-RAY DIFFRACTIONr_chiral_restr0.1090.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212340
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02477
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.4875.7371052
X-RAY DIFFRACTIONr_mcbond_other5.4865.7361051
X-RAY DIFFRACTIONr_mcangle_it7.8688.5651308
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.1796.491119
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.773→2.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 54 -
Rwork0.321 1085 -
obs--90.54 %

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