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- PDB-1h6e: MU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLE... -

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Basic information

Entry
Database: PDB / ID: 1h6e
TitleMU2 ADAPTIN SUBUNIT (AP50) OF AP2 ADAPTOR (SECOND DOMAIN), COMPLEXED WITH CTLA-4 INTERNALIZATION PEPTIDE TTGVYVKMPPT
Components
  • CLATHRIN COAT ASSEMBLY PROTEIN AP50
  • CYTOTOXIC T-LYMPHOCYTE PROTEIN 4
KeywordsENDOCYTOSIS/EXOCYTOSIS / ENDOCYTOSIS / ADAPTOR / PEPTIDE COMPLEX / PHOSPHORYLATION / ENDOCYTOSIS-EXOCYTOSIS complex
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / protein complex involved in cell adhesion / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 ...Nef mediated downregulation of CD28 cell surface expression / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / LDL clearance / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / protein complex involved in cell adhesion / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / negative regulation of regulatory T cell differentiation / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / regulation of vesicle size / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / vesicle budding from membrane / Formation of annular gap junctions / clathrin-dependent endocytosis / Gap junction degradation / signal sequence binding / Nef Mediated CD4 Down-regulation / Co-stimulation by CD28 / endolysosome membrane / low-density lipoprotein particle receptor binding / Co-inhibition by CTLA4 / negative regulation of B cell proliferation / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of receptor internalization / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / negative regulation of T cell proliferation / vesicle-mediated transport / clathrin-coated pit / MHC class II antigen presentation / VLDLR internalisation and degradation / B cell receptor signaling pathway / intracellular protein transport / clathrin-coated endocytic vesicle membrane / receptor internalization / cytoplasmic side of plasma membrane / endocytosis / terminal bouton / disordered domain specific binding / synaptic vesicle / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / T cell receptor signaling pathway / Clathrin-mediated endocytosis / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / adaptive immune response / transmembrane transporter binding / postsynapse / immune response / positive regulation of apoptotic process / lysosomal membrane / external side of plasma membrane / DNA damage response / lipid binding / perinuclear region of cytoplasm / glutamatergic synapse / Golgi apparatus / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Mu homology domain, subdomain B / Cytotoxic T-lymphocyte protein 4/CD28 / 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. / : ...Cytotoxic T-lymphocyte antigen 4 / Mu homology domain, subdomain B / Cytotoxic T-lymphocyte protein 4/CD28 / 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. / : / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / 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 V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cytotoxic T-lymphocyte protein 4 / AP-2 complex subunit mu / AP-2 complex subunit mu
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.6 Å
AuthorsRowsell, S. / Pauptit, R.A.
Citation
Journal: Biochem.J. / Year: 2001
Title: Study of the Interaction of the Medium Chain Mu2 Subunit of the Clathrin-Associated Adapter Protein Complex 2 with Cytotoxic T-Lymphocyte Antigen 4 and Cd28
Authors: Follows, E.R. / Mcpheat, J.C. / Minshull, C. / Moore, N.C. / Pauptit, R.A. / Rowsell, S. / Stacey, C.L. / Stanway, J.J. / Taylor, I.W. / Abbott, W.M.
#1: Journal: Science / Year: 1998
Title: A Structural Explanation for the Recognition of Tyrosine-Based Endocytotic Signals
Authors: Owen, D.J. / Evans, P.R.
History
DepositionJun 12, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Source and taxonomy / Version format compliance
Revision 2.0May 29, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Experimental preparation / Other
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 2.1Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLATHRIN COAT ASSEMBLY PROTEIN AP50
P: CYTOTOXIC T-LYMPHOCYTE PROTEIN 4


Theoretical massNumber of molelcules
Total (without water)34,2092
Polymers34,2092
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)126.779, 126.779, 74.161
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 CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT ASSOCIATED PROTEIN AP50 / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / HA2 50 KDA ...CLATHRIN COAT ASSOCIATED PROTEIN AP50 / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / HA2 50 KDA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM CHAIN / AP-2 MU 2 CHAIN / AP50


Mass: 33014.516 Da / Num. of mol.: 1 / Fragment: INTERNALIZATION SIGNAL BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: THE FIRST 16 RESIDUES OF THE POLYMER MAKE UP A 6HIS-CMYC-TAG (HHHHHHEQKLISEEDL)
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P20172, UniProt: Q96CW1*PLUS
#2: Protein/peptide CYTOTOXIC T-LYMPHOCYTE PROTEIN 4 / CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED ANTIGEN 4 / CTLA-4 / CD152 ANTIGEN


Mass: 1194.419 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: 11-MER INTERNALISATION SIGNAL MOTIF FROM CTLA-4 (HOMO SAPIENS), TTGVYVKMPPT
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P16410

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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: 5.03 Å3/Da / Density % sol: 75 % / Description: ISOMORPHOUS TO 1BXX
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROPS CONTAINING A 1:1 MIXTURE OF COMPLEX SOLUTION 6MG/ML PROTEIN AND 1MM 11MER PEPTIDE SOLUTION IN 20MM HEPES PH7.5, 1MM DTT AND RESERVOIR BUFFER 1.4-2.4M SODIUM CHLORIDE, 0.1M MES ...Details: HANGING DROPS CONTAINING A 1:1 MIXTURE OF COMPLEX SOLUTION 6MG/ML PROTEIN AND 1MM 11MER PEPTIDE SOLUTION IN 20MM HEPES PH7.5, 1MM DTT AND RESERVOIR BUFFER 1.4-2.4M SODIUM CHLORIDE, 0.1M MES PH6.2-7.0, 0.4M NA/K PHOSPHATE, 15% GLYCEROL, pH 7.00
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
16 mg/mlprotein1drop
21 mMpeptide1drop
320 mMHEPES1droppH7.5
41 mMdithiothreitol1drop
50.1 MMES1reservoirpH6.2-7.0
61.4-2.4 M1reservoirNaCl
70.4 Msodium potassium phosphate1reservoir
815 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 26, 1999 / Details: MIRROR
RadiationMonochromator: YES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 3.6→48.2 Å / Num. obs: 6681 / % possible obs: 83.2 % / Redundancy: 2.2 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 4
Reflection shellResolution: 3.6→3.8 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 1.7 / % possible all: 85.9
Reflection
*PLUS
Num. measured all: 14633
Reflection shell
*PLUS
% possible obs: 85.9 % / Num. unique obs: 992 / Num. measured obs: 2081

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Processing

Software
NameVersionClassification
CNX2000refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1BXX

1bxx


Resolution: 3.6→7.99 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.317 603 11.2 %RANDOM
Rwork0.278 ---
obs-5400 74.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.14399 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a1.21 Å1.44 Å
Refinement stepCycle: LAST / Resolution: 3.6→7.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 0 0 1817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.6→3.8 Å / Rfactor Rfree error: 0.067 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.566 72 10.4 %
Rwork0.626 619 -
obs--57.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Refinement
*PLUS
Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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