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- PDB-6qh7: AP2 clathrin adaptor mu2T156-phosphorylated core with two cargo p... -

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Basic information

Entry
Database: PDB / ID: 6qh7
TitleAP2 clathrin adaptor mu2T156-phosphorylated core with two cargo peptides in open+ conformation
Components
  • (AP-2 complex subunit ...) x 3
  • ADAPTOR-RELATED PROTEIN COMPLEX 2, MU 2 SUBUNIT, C-TERMINAL DOMAIN
  • CD4 CARGO PEPTIDE
  • TGN38 CARGO PEPTIDE
KeywordsPROTEIN TRANSPORT / ENDOCYTOSIS / PHOSPHORYLATION / CELL MEMBRANE
Function / homology
Function and homology information


Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Gap junction degradation / Formation of annular gap junctions ...Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Gap junction degradation / Formation of annular gap junctions / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Retrograde neurotrophin signalling / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Trafficking of GluR2-containing AMPA receptors / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / MHC class II antigen presentation / clathrin adaptor complex / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD4 / Recycling pathway of L1 / extrinsic component of presynaptic endocytic zone membrane / MHC class II antigen presentation / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / regulation of vesicle size / AP-2 adaptor complex / postsynaptic endocytic zone / postsynaptic neurotransmitter receptor internalization / response to methamphetamine hydrochloride / Cargo recognition for clathrin-mediated endocytosis / maintenance of protein location in cell / cellular response to ionomycin / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Retrograde neurotrophin signalling / T cell selection / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / MHC class II protein binding / vesicle budding from membrane / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / MHC class II antigen presentation / positive regulation of kinase activity / signal sequence binding / interleukin-15-mediated signaling pathway / cellular response to granulocyte macrophage colony-stimulating factor stimulus / coronary vasculature development / positive regulation of monocyte differentiation / positive regulation of protein localization to membrane / Nef Mediated CD4 Down-regulation / Alpha-defensins / endolysosome membrane / neurotransmitter secretion / response to vitamin D / regulation of T cell activation / extracellular matrix structural constituent / aorta development / ventricular septum development / Other interleukin signaling / Neutrophil degranulation / low-density lipoprotein particle receptor binding / T cell receptor complex / clathrin binding / enzyme-linked receptor protein signaling pathway / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / positive regulation of calcium ion transport into cytosol / positive regulation of protein kinase activity / regulation of calcium ion transport / positive regulation of endocytosis / positive regulation of receptor internalization / Generation of second messenger molecules / macrophage differentiation / T cell differentiation / immunoglobulin binding / synaptic vesicle endocytosis / EPH-ephrin mediated repulsion of cells / Co-inhibition by PD-1 / Binding and entry of HIV virion / negative regulation of protein localization to plasma membrane
Similarity search - Function
Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain ...Beta-Lactamase - #60 / Mu homology domain, subdomain B / AP-2 complex subunit sigma / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / Mu2, C-terminal domain / AP-2 complex subunit mu, N-terminal / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta2-adaptin appendage, C-terminal sub-domain / AP-1/2/4 complex subunit beta / Adaptor protein complex, sigma subunit / : / Beta-adaptin appendage, C-terminal subdomain / Beta2-adaptin appendage, C-terminal sub-domain / CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / AP complex subunit beta / Clathrin adaptor complex, small chain / Clathrin adaptor complexes small chain signature. / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor, mu subunit / Immunoglobulin C2-set / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / Immunoglobulin C2-set domain / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Adaptin C-terminal domain / Adaptin C-terminal domain / AP complex, mu/sigma subunit / Adaptor complexes medium subunit family / Clathrin adaptor complex small chain / AP-2 complex subunit mu, C-terminal superfamily / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Longin-like domain superfamily / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Immunoglobulin / Immunoglobulin domain / Leucine-rich Repeat Variant / Beta-Lactamase / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Armadillo-like helical / Alpha Horseshoe / Immunoglobulin subtype / Immunoglobulin / Armadillo-type fold / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
T-cell surface glycoprotein CD4 / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / AP-2 complex subunit mu / AP-2 complex subunit alpha
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsWrobel, A.G. / Owen, D.J. / McCoy, A.J. / Evans, P.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust090909/Z/09/Z United Kingdom
Wellcome Trust097040/Z/11/Z United Kingdom
CitationJournal: Dev.Cell / Year: 2019
Title: Temporal Ordering in Endocytic Clathrin-Coated Vesicle Formation via AP2 Phosphorylation.
Authors: Wrobel, A.G. / Kadlecova, Z. / Kamenicky, J. / Yang, J.C. / Herrmann, T. / Kelly, B.T. / McCoy, A.J. / Evans, P.R. / Martin, S. / Muller, S. / Sroubek, F. / Neuhaus, D. / Honing, S. / Owen, D.J.
History
DepositionJan 15, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AP-2 complex subunit alpha
B: AP-2 complex subunit beta
M: ADAPTOR-RELATED PROTEIN COMPLEX 2, MU 2 SUBUNIT, C-TERMINAL DOMAIN
N: ADAPTOR-RELATED PROTEIN COMPLEX 2, MU 2 SUBUNIT, C-TERMINAL DOMAIN
P: TGN38 CARGO PEPTIDE
Q: CD4 CARGO PEPTIDE
S: AP-2 complex subunit sigma


Theoretical massNumber of molelcules
Total (without water)257,9847
Polymers257,9847
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16240 Å2
ΔGint-61 kcal/mol
Surface area72580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.177, 182.177, 211.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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AP-2 complex subunit ... , 3 types, 3 molecules ABS

#1: Protein AP-2 complex subunit alpha


Mass: 69642.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2a2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66HM2, UniProt: P18484*PLUS
#2: Protein AP-2 complex subunit beta / AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta ...AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta / Beta-2-adaptin / Beta-adaptin / Clathrin assembly protein complex 2 beta large chain / Plasma membrane adaptor HA2/AP2 adaptin beta subunit


Mass: 67091.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AP2B1, ADTB2, CLAPB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P63010
#6: Protein AP-2 complex subunit sigma / Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / ...Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / Clathrin assembly protein 2 sigma small chain / Clathrin coat assembly protein AP17 / Clathrin coat-associated protein AP17 / Plasma membrane adaptor AP-2 17 kDa protein / Sigma-adaptin 3b / Sigma2-adaptin


Mass: 17038.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2s1, Ap17, Claps2 / Production host: Escherichia coli (E. coli) / References: UniProt: P62743, UniProt: P62744*PLUS

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Protein , 1 types, 2 molecules MN

#3: Protein ADAPTOR-RELATED PROTEIN COMPLEX 2, MU 2 SUBUNIT, C-TERMINAL DOMAIN


Mass: 51044.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZC13, UniProt: P84092*PLUS

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Protein/peptide , 2 types, 2 molecules PQ

#4: Protein/peptide TGN38 CARGO PEPTIDE


Mass: 808.860 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: YXXPhi INTERNALISATION SIGNAL MOTIF / Source: (synth.) Homo sapiens (human)
#5: Protein/peptide CD4 CARGO PEPTIDE


Mass: 1314.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ACIDIC DILEUCINE INTERNALISATION SIGNAL MOTIF / Source: (synth.) Homo sapiens (human) / References: UniProt: P01730*PLUS

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Details

Has protein modificationY

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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: 3.4 Å3/Da / Density % sol: 63.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 7.5% PVA, 9% 1-propanol, 90 mM Hepes pH 7.4, 100 mM guanidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.4→110 Å / Num. obs: 49558 / % possible obs: 99.9 % / Redundancy: 13.88 % / Biso Wilson estimate: 100 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.28 / Rrim(I) all: 0.29 / Net I/σ(I): 8.8
Reflection shellResolution: 3.4→3.5 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→110 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 31.856 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24815 2529 5.1 %RANDOM
Rwork0.20777 ---
obs0.20986 46920 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 143.733 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.54 Å2
Refinement stepCycle: 1 / Resolution: 3.4→110 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13342 0 0 0 13342
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913580
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213024
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.97318385
X-RAY DIFFRACTIONr_angle_other_deg1.022330187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55151663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86624.33612
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.883152497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2341589
X-RAY DIFFRACTIONr_chiral_restr0.0820.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02114825
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022660
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_it9.80414.4726676
X-RAY DIFFRACTIONr_mcbond_other9.80314.4726675
X-RAY DIFFRACTIONr_mcangle_it15.10521.6868331
X-RAY DIFFRACTIONr_mcangle_other15.10421.6868332
X-RAY DIFFRACTIONr_scbond_it9.21614.9486904
X-RAY DIFFRACTIONr_scbond_other9.21414.9466901
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.8522.19510053
X-RAY DIFFRACTIONr_long_range_B_refined22.63353930
X-RAY DIFFRACTIONr_long_range_B_other22.63353931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.429 172 -
Rwork0.414 3393 -
obs--98.89 %

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