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- PDB-2vgl: AP2 CLATHRIN ADAPTOR CORE -

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Basic information

Entry
Database: PDB / ID: 2vgl
TitleAP2 CLATHRIN ADAPTOR CORE
Components
  • (AP-2 COMPLEX SUBUNIT ...) x 3
  • ADAPTOR PROTEIN COMPLEX AP-2, ALPHA 2 SUBUNIT
KeywordsPROTEIN TRANSPORT / CYTOPLASMIC VESICLE / ALTERNATIVE SPLICING / ENDOCYTOSIS / LIPID-BINDING / GOLGI APPARATUS / ADAPTOR / MEMBRANE / TRANSPORT / COATED PIT / PHOSPHORYLATION
Function / homology
Function and homology information


secretory vesicle / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance ...secretory vesicle / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Gap junction degradation / Formation of annular gap junctions / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Nef Mediated CD8 Down-regulation / Trafficking of GluR2-containing AMPA receptors / LDL clearance / Retrograde neurotrophin signalling / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / 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 / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / Recycling pathway of L1 / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / Cargo recognition for clathrin-mediated endocytosis / clathrin adaptor activity / Clathrin-mediated endocytosis / LDL clearance / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / coronary vasculature development / Nef Mediated CD4 Down-regulation / positive regulation of protein localization to membrane / neurotransmitter secretion / endolysosome membrane / aorta development / Neutrophil degranulation / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / Trafficking of GluR2-containing AMPA receptors / Recycling pathway of L1 / positive regulation of receptor internalization / positive regulation of endocytosis / EPH-ephrin mediated repulsion of cells / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / clathrin-coated pit / phosphatidylinositol binding / MHC class II antigen presentation / protein serine/threonine kinase binding / VLDLR internalisation and degradation / intracellular protein transport / kidney development / clathrin-coated endocytic vesicle membrane / receptor internalization / kinase binding / cytoplasmic side of plasma membrane / terminal bouton / disordered domain specific binding / synaptic vesicle / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / protein-containing complex assembly / cytoplasmic vesicle / Potential therapeutics for SARS / transmembrane transporter binding / postsynapse / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / membrane / plasma membrane / cytosol
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 / 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 / Clathrin adaptor, mu subunit, conserved site / Clathrin adaptor complexes medium chain signature 2. / : / 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 / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / AP-2 complex subunit mu, C-terminal superfamily / 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 / Leucine-rich Repeat Variant / Beta-Lactamase / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
INOSITOL HEXAKISPHOSPHATE / AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit beta / AP-2 complex subunit mu / AP-2 complex subunit alpha
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
HOMO SAPIENS (human)
MUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsOwen, D.J. / Collins, B.M. / McCoy, A.J. / Evans, P.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Molecular Architecture and Functional Model of the Endocytic Ap2 Complex
Authors: Collins, B.M. / Mccoy, A.J. / Kent, H.M. / Evans, P.R. / Owen, D.J.
History
DepositionNov 14, 2007Deposition site: PDBE / Processing site: PDBE
SupersessionDec 25, 2007ID: 1GW5
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 7, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: ADAPTOR PROTEIN COMPLEX AP-2, ALPHA 2 SUBUNIT
B: AP-2 COMPLEX SUBUNIT BETA-1
M: AP-2 COMPLEX SUBUNIT MU-1
S: AP-2 COMPLEX SUBUNIT SIGMA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,0355
Polymers203,3754
Non-polymers6601
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21720 Å2
ΔGint-105.4 kcal/mol
Surface area88170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)121.746, 121.746, 258.124
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ADAPTOR PROTEIN COMPLEX AP-2, ALPHA 2 SUBUNIT


Mass: 69656.297 Da / Num. of mol.: 1 / Fragment: 1-621
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q66HM2, UniProt: P18484*PLUS

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AP-2 COMPLEX SUBUNIT ... , 3 types, 3 molecules BMS

#2: Protein AP-2 COMPLEX SUBUNIT BETA-1 / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ...ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-1 SUBUNIT / BETA-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B


Mass: 66953.195 Da / Num. of mol.: 1 / Fragment: 1-591
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PMW172H6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P63010
#3: Protein AP-2 COMPLEX SUBUNIT MU-1 / ADAPTIN MU-1 / AP-2 MU-2 CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT-ASSOCIATED ...ADAPTIN MU-1 / AP-2 MU-2 CHAIN / CLATHRIN COAT ASSEMBLY PROTEIN AP50 / CLATHRIN COAT-ASSOCIATED PROTEIN AP50 / PLASMA MEMBRANE ADAPTOR AP-2 50 KDA PROTEIN / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 MEDIUM 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(DE3)PLYSS / References: UniProt: P84092
#4: Protein AP-2 COMPLEX SUBUNIT SIGMA-1 / ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA-1 SUBUNIT / SIGMA-ADAPTIN 3B / CLATHRIN COAT ASSEMBLY ...ADAPTER-RELATED PROTEIN COMPLEX 2 SIGMA-1 SUBUNIT / SIGMA-ADAPTIN 3B / CLATHRIN COAT ASSEMBLY PROTEIN AP17 / CLATHRIN COAT-ASSOCIATED PROTEIN AP17 / PLASMA MEMBRANE ADAPTOR AP-2 17 KDA PROTEIN / CLATHRIN ASSEMBLY PROTEIN 2 SMALL CHAIN


Mass: 17038.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PMW172K / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P62743

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Non-polymers , 2 types, 13 molecules

#5: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.87 Å3/Da / Density % sol: 56.76 % / Description: NONE
Crystal growpH: 6.2
Details: 18% PEG, 10MM NA/K PHOSPHATE PH 6.2, 200MM NACL, 4MM DTT, IP6
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
218 %PEG10001reservoir
3100 mMsodium potassium phosphate1reservoirpH6.2
4200 mM1reservoirNaCl
54 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 15, 2001 / Details: MIRRORS
RadiationMonochromator: GE220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→67.42 Å / Num. obs: 66642 / % possible obs: 99.39 % / Observed criterion σ(I): 6 / Redundancy: 5.63 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.0515
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.27 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.16 / % possible all: 98.44
Reflection
*PLUS
Highest resolution: 2.6 Å / % possible obs: 99.4 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
% possible obs: 99.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→66.67 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.847 / Cross valid method: THROUGHOUT / ESU R: 0.804 / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.339 3498 5.1 %RANDOM
Rwork0.261 ---
obs0.265 65198 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.09 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20.51 Å20 Å2
2--1.01 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 2.6→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13707 0 36 12 13755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02213990
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.97618949
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.02551710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.5924.297626
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.523152576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.971592
X-RAY DIFFRACTIONr_chiral_restr0.0880.22204
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210296
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.290.26935
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.29602
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2549
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5480.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6861.58587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.248213953
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.65935403
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5614.54996
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: 2.6→2.66 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.441 257 -
Rwork0.358 4691 -
obs--98.1 %
Refinement
*PLUS
Rfactor obs: 0.26 / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: r_bond_d / Dev ideal: 0.028

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