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- PDB-2iv9: B2-appendage from AP2 in complex with Eps15 peptide -

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Basic information

Entry
Database: PDB / ID: 2iv9
TitleB2-appendage from AP2 in complex with Eps15 peptide
Components
  • AP-2 COMPLEX SUBUNIT BETA-2
  • EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15 ISOFORM B
KeywordsENDOCYTOSIS/REGULATOR / ALTERNATIVE SPLICING / ENDOCYTOSIS-REGULATOR COMPLEX / B2 / EAR / EPS15 / ADAPTOR / CALCIUM / APPENDAGE / COATED PITS / ENDOCYTOSIS / PHOSPHORYLATION
Function / homology
Function and homology information


Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / Golgi to endosome transport / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex / vesicle organization / postsynaptic neurotransmitter receptor internalization ...Nef Mediated CD8 Down-regulation / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / clathrin adaptor complex / Trafficking of GluR2-containing AMPA receptors / Golgi to endosome transport / WNT5A-dependent internalization of FZD4 / clathrin coat of coated pit / AP-2 adaptor complex / vesicle organization / postsynaptic neurotransmitter receptor internalization / clathrin coat assembly / Retrograde neurotrophin signalling / clathrin-coated endocytic vesicle / LDL clearance / clathrin-dependent endocytosis / coronary vasculature development / endocytic recycling / signal sequence binding / endolysosome membrane / Nef Mediated CD4 Down-regulation / aggresome / aorta development / ciliary membrane / clathrin-coated vesicle / ventricular septum development / endosomal transport / clathrin binding / positive regulation of receptor recycling / Recycling pathway of L1 / synaptic vesicle endocytosis / polyubiquitin modification-dependent protein binding / EPH-ephrin mediated repulsion of cells / clathrin-coated pit / vesicle-mediated transport / MHC class II antigen presentation / VLDLR internalisation and degradation / basal plasma membrane / InlB-mediated entry of Listeria monocytogenes into host cell / kidney development / EGFR downregulation / clathrin-coated endocytic vesicle membrane / intracellular protein transport / Negative regulation of MET activity / cytoplasmic side of plasma membrane / SH3 domain binding / endocytosis / endocytic vesicle membrane / protein transport / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / regulation of cell population proliferation / early endosome membrane / postsynapse / Potential therapeutics for SARS / receptor-mediated endocytosis of virus by host cell / early endosome / cadherin binding / symbiont entry into host cell / apical plasma membrane / intracellular membrane-bounded organelle / glutamatergic synapse / synapse / calcium ion binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #1150 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain ...Immunoglobulin-like - #1150 / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain / Beta-adaptin appendage, C-terminal subdomain / AP-1/2/4 complex subunit beta / Beta2-adaptin appendage, C-terminal sub-domain / Beta2-adaptin appendage, C-terminal sub-domain / AP complex subunit beta / 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 / Clathrin/coatomer adaptor, adaptin-like, N-terminal / Adaptin N terminal region / Clathrin adaptor, appendage, Ig-like subdomain superfamily / Ubiquitin-interacting motif. / TATA-Binding Protein / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / TBP domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Armadillo-like helical / EF-hand domain pair / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor substrate 15 / AP-2 complex subunit beta / Epidermal growth factor receptor pathway substrate 15 isoform B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
RATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFord, M.G.J. / Schmid, E.M. / McMahon, H.T.
CitationJournal: Plos Biol. / Year: 2006
Title: Role of the Ap2 Beta-Appendage Hub in Recruiting Partners for Clathrin-Coated Vesicle Assembly
Authors: Schmid, E.M. / Ford, M.G.J. / Burtey, A. / Praefcke, G.J.K. / Peak-Chew, S.-Y. / Mills, I.G. / Benmerah, A. / Mcmahon, H.T.
History
DepositionJun 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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: AP-2 COMPLEX SUBUNIT BETA-2
B: AP-2 COMPLEX SUBUNIT BETA-2
P: EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15 ISOFORM B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3506
Polymers55,0613
Non-polymers2883
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.498, 72.180, 116.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AP-2 COMPLEX SUBUNIT BETA-2 / BETA2-APPENDAGE / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-2 SUBUNIT / BETA-ADAPTIN / PLASMA MEMBRANE ...BETA2-APPENDAGE / ADAPTER-RELATED PROTEIN COMPLEX 2 BETA-2 SUBUNIT / BETA-ADAPTIN / PLASMA MEMBRANE ADAPTOR HA2/AP2 ADAPTIN BETA SUBUNIT / CLATHRIN ASSEMBLY PROTEIN COMPLEX 2 BETA LARGE CHAIN / AP105B


Mass: 26899.055 Da / Num. of mol.: 2 / Fragment: APPENDAGE DOMAIN, RESIDUES 700-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-15B / Production host: ESCHERICIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P63010
#2: Protein/peptide EPIDERMAL GROWTH FACTOR RECEPTOR SUBSTRATE 15 ISOFORM B / EPS15 / PROTEIN EPS15 / AF-1P PROTEIN


Mass: 1263.311 Da / Num. of mol.: 1 / Fragment: RESIDUES 720-731 / Source method: obtained synthetically / Source: (synth.) RATTUS NORVEGICUS (Norway rat) / References: UniProt: Q5JC29, UniProt: P42566*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47 %
Crystal growpH: 4.5 / Details: 2M AMMONIUM SULPHATE, 0.1M AMMONIUM ACETATE PH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 12, 2006 / Details: BENT MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→45.31 Å / Num. obs: 38753 / % possible obs: 97.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E42 CHAIN A

1e42


Resolution: 1.9→45.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.218 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME DENSITY WAS SEEN FOR THE KEY BINDING RESIDUES AT THE EPS15 P-SHORT BINDING SITE ON MOLECULE B BUT A MODEL COULD NOT BE BUILT UNAMBIGUOSLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1946 5 %RANDOM
Rwork0.214 ---
obs0.216 36750 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 15 252 4053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223936
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9615367
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.68925.706177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88715676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.388159
X-RAY DIFFRACTIONr_chiral_restr0.0860.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022976
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21581
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22636
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8021.52510
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36923948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.61431638
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5564.51412
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 108
Rwork0.263 2187

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