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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 SUBUNITAdapter
KeywordsPROTEIN TRANSPORT / CYTOPLASMIC VESICLE / ALTERNATIVE SPLICING / ENDOCYTOSIS / LIPID-BINDING / GOLGI APPARATUS / ADAPTOR / MEMBRANE / TRANSPORT / COATED PIT / PHOSPHORYLATION
Function / homology
Function and homology information


WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / EPH-ephrin mediated repulsion of cells / MHC class II antigen presentation / Nef Mediated CD8 Down-regulation / Retrograde neurotrophin signalling / Nef Mediated CD4 Down-regulation / Cargo recognition for clathrin-mediated endocytosis / WNT5A-dependent internalization of FZD4 ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / EPH-ephrin mediated repulsion of cells / MHC class II antigen presentation / Nef Mediated CD8 Down-regulation / Retrograde neurotrophin signalling / Nef Mediated CD4 Down-regulation / Cargo recognition for clathrin-mediated endocytosis / WNT5A-dependent internalization of FZD4 / VLDLR internalisation and degradation / LDL clearance / VLDLR internalisation and degradation / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / Neutrophil degranulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Recycling pathway of L1 / Trafficking of GluR2-containing AMPA receptors / MHC class II antigen presentation / Formation of annular gap junctions / Gap junction degradation / Clathrin-mediated endocytosis / LDL clearance / Retrograde neurotrophin signalling / Recycling pathway of L1 / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / VLDLR internalisation and degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Retrograde neurotrophin signalling / WNT5A-dependent internalization of FZD4 / MHC class II antigen presentation / Trafficking of GluR2-containing AMPA receptors / clathrin adaptor activity / low-density lipoprotein particle receptor catabolic process / AP-2 adaptor complex / positive regulation of protein localization to membrane / postsynaptic neurotransmitter receptor internalization / coronary vasculature development / positive regulation of synaptic vesicle endocytosis / clathrin coat assembly / endolysosome membrane / signal sequence binding / clathrin-dependent endocytosis / low-density lipoprotein particle clearance / clathrin-coated endocytic vesicle / aorta development / clathrin binding / positive regulation of endocytosis / ventricular septum development / positive regulation of receptor internalization / clathrin-coated endocytic vesicle membrane / low-density lipoprotein particle receptor binding / synaptic vesicle endocytosis / Wnt signaling pathway, planar cell polarity pathway / phosphatidylinositol binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / presynapse / vesicle-mediated transport / negative regulation of neuron death / terminal bouton / endocytic vesicle membrane / ephrin receptor signaling pathway / intracellular protein transport / regulation of defense response to virus by virus / postsynapse / synaptic vesicle / protein-containing complex assembly / membrane organization / disordered domain specific binding / lipid binding / protein-containing complex binding / intracellular membrane-bounded organelle / glutamatergic synapse / protein kinase binding / membrane / plasma membrane / cytosol
AP-1/2/4 complex subunit beta / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / AP complex, mu/sigma subunit / Clathrin adaptor, mu subunit, conserved site / Adaptor protein complex AP-2, alpha subunit / Adaptor protein complex, sigma subunit / Armadillo-type fold / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TBP domain superfamily ...AP-1/2/4 complex subunit beta / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / AP complex, mu/sigma subunit / Clathrin adaptor, mu subunit, conserved site / Adaptor protein complex AP-2, alpha subunit / Adaptor protein complex, sigma subunit / Armadillo-type fold / Beta-adaptin appendage, C-terminal subdomain / Clathrin adaptor, appendage, Ig-like subdomain superfamily / TBP domain superfamily / AP-2 complex subunit sigma / Armadillo-like helical / Longin-like domain superfamily / Coatomer/calthrin adaptor appendage, C-terminal subdomain / Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Clathrin adaptor, mu subunit / Clathrin adaptor complex, small chain / AP complex subunit beta / Mu homology domain / Mu homology domain (MHD) profile. / Clathrin adaptor complexes medium chain signature 2. / AP-2 complex subunit mu, C-terminal superfamily / Clathrin adaptor complexes medium chain signature 1. / Clathrin adaptor complexes small chain signature. / Beta2-adaptin appendage, C-terminal sub-domain / Adaptin C-terminal domain / Alpha adaptin AP2, C-terminal domain / Adaptin N terminal region / Clathrin adaptor complex small chain / Adaptor complexes medium subunit family / Armadillo
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
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.
Validation Report
SummaryFull reportAbout validation report
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

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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


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21720 Å2
ΔGint-105.4 kcal/mol
Surface area88170 Å2
MethodPQS
Unit cell
γ
α
β
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/peptide , 1 types, 1 molecules A

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


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/peptide AP-2 COMPLEX SUBUNIT BETA-1 / 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/peptide AP-2 COMPLEX SUBUNIT MU-1 / 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/peptide AP-2 COMPLEX SUBUNIT SIGMA-1 / 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


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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O / Water

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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

Crystal-ID: 1

IDConc.Common nameSol-IDDetailsChemical formula
115 mg/mlproteindrop
218 %PEG1000reservoir
3100 mMsodium potassium phosphatereservoirpH6.2
4200 mMreservoirNaCl
54 mMdithiothreitolreservoir

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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

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0180.02213990
r_bond_other_d
r_angle_refined_deg1.7021.97618949
r_angle_other_deg
r_dihedral_angle_1_deg8.02551710
r_dihedral_angle_2_deg40.5924.297626
r_dihedral_angle_3_deg19.523152576
r_dihedral_angle_4_deg18.971592
r_chiral_restr0.0880.22204
r_gen_planes_refined0.0060.0210296
r_gen_planes_other
r_nbd_refined0.290.26935
r_nbd_other
r_nbtor_refined0.3250.29602
r_nbtor_other
r_xyhbond_nbd_refined0.1990.2549
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.5480.261
r_symmetry_vdw_other
r_symmetry_hbond_refined0.3390.21
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.6861.58587
r_mcbond_other
r_mcangle_it1.248213953
r_mcangle_other
r_scbond_it1.65935403
r_scbond_other
r_scangle_it2.5614.54996
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_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
Refine LS restraints
*PLUS
Type: r_bond_d / Dev ideal: 0.028

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