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- PDB-3hs8: Intersectin 1-peptide-AP2 alpha ear complex -

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Basic information

Entry
Database: PDB / ID: 3hs8
TitleIntersectin 1-peptide-AP2 alpha ear complex
Components
  • Adaptor protein complex AP-2, alpha 2 subunit
  • peptide from Intersectin-1, residues 840-851
KeywordsENDOCYTOSIS / adaptor complex AP-2 / Cell membrane / Coated pit / Lipid-binding / Membrane / Disease mutation / Transferase
Function / homology
Function and homology information


presynaptic endocytic zone / RHOQ GTPase cycle / clathrin-dependent synaptic vesicle endocytosis / CDC42 GTPase cycle / positive regulation of caveolin-mediated endocytosis / NRAGE signals death through JNK / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Retrograde neurotrophin signalling ...presynaptic endocytic zone / RHOQ GTPase cycle / clathrin-dependent synaptic vesicle endocytosis / CDC42 GTPase cycle / positive regulation of caveolin-mediated endocytosis / NRAGE signals death through JNK / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Retrograde neurotrophin signalling / EPHB-mediated forward signaling / Trafficking of GluR2-containing AMPA receptors / VLDLR internalisation and degradation / G alpha (12/13) signalling events / Recycling pathway of L1 / postsynaptic endocytic zone / positive regulation of growth hormone secretion / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / RHOG GTPase cycle / Cargo recognition for clathrin-mediated endocytosis / membrane coat / Clathrin-mediated endocytosis / clathrin-cargo adaptor activity / regulation of modification of postsynaptic actin cytoskeleton / clathrin-dependent endocytosis / MHC class II antigen presentation / apical dendrite / postsynaptic actin cytoskeleton / proline-rich region binding / kinase activator activity / regulation of postsynapse organization / regulation of hematopoietic stem cell differentiation / endosomal transport / small GTPase-mediated signal transduction / intracellular vesicle / positive regulation of dendritic spine development / exocytosis / endocytic vesicle / synaptic vesicle endocytosis / vesicle-mediated transport / Neutrophil degranulation / clathrin-coated pit / guanyl-nucleotide exchange factor activity / secretory granule / calyx of Held / intracellular protein transport / recycling endosome / cytoplasmic side of plasma membrane / kinase binding / endocytosis / disordered domain specific binding / intracellular protein localization / nuclear envelope / cell-cell signaling / lamellipodium / protein transport / presynapse / presynaptic membrane / cytoplasmic vesicle / protein-macromolecule adaptor activity / dendritic spine / negative regulation of neuron apoptotic process / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / postsynapse / protein domain specific binding / neuronal cell body / calcium ion binding / lipid binding / protein kinase binding / glutamatergic synapse / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / : / Gamma-adaptin ear (GAE) domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / EH domain / EH domain profile. ...Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / : / Gamma-adaptin ear (GAE) domain / Clathrin adaptor, alpha-adaptin, appendage, C-terminal subdomain / Adaptor protein complex AP-2, alpha subunit / Alpha adaptin AP2, C-terminal domain / EH domain / EH domain profile. / Eps15 homology domain / EH domain / TATA-Binding Protein / : / Guanine-nucleotide dissociation stimulator, CDC24, conserved site / Dbl homology (DH) domain signature. / 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 / TATA-Binding Protein / Variant SH3 domain / Variant SH3 domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / TBP domain superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 / PH-like domain superfamily / Armadillo-type fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AP-2 complex subunit alpha-2 / AP-2 complex subunit alpha / Intersectin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsVahedi-Faridi, A. / Pechstein, A. / Schaefer, J.G. / Saenger, W. / Haucke, V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Regulation of synaptic vesicle recycling by complex formation between intersectin 1 and the clathrin adaptor complex AP2.
Authors: Pechstein, A. / Bacetic, J. / Vahedi-Faridi, A. / Gromova, K. / Sundborger, A. / Tomlin, N. / Krainer, G. / Vorontsova, O. / Schafer, J.G. / Owe, S.G. / Cousin, M.A. / Saenger, W. / Shupliakov, O. / Haucke, V.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
P: peptide from Intersectin-1, residues 840-851


Theoretical massNumber of molelcules
Total (without water)32,1662
Polymers32,1662
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-4 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.484, 120.412, 32.220
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Adaptor protein complex AP-2, alpha 2 subunit


Mass: 30744.889 Da / Num. of mol.: 1 / Fragment: UNP residues 702-938
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2a2 / Plasmid: pET-28(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PEE6, UniProt: P17427*PLUS
#2: Protein/peptide peptide from Intersectin-1, residues 840-851


Mass: 1421.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q9Z0R4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.94 Å3/Da / Density % sol: 36.74 % / Mosaicity: 0.709 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG4000, 100mM HEPES, 10% Isopropanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 19195 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.03 / Χ2: 0.733 / Net I/σ(I): 27.513
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.972.50.1316300.838183.2
1.97-2.052.80.11318760.815192.7
2.05-2.142.90.07918370.748191.2
2.14-2.252.90.06318720.736192.3
2.25-2.3930.05218880.721192.4
2.39-2.5830.04218950.704192.6
2.58-2.8430.03319570.677195.3
2.84-3.2530.02720470.741198.6
3.25-4.0930.02820790.565199
4.09-402.90.01921140.836194.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.05 Å31.12 Å
Translation2.05 Å31.12 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30.1 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.226 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.845 / SU B: 7.717 / SU ML: 0.104 / SU R Cruickshank DPI: 0.208 / SU Rfree: 0.173 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1000 5.2 %RANDOM
Rwork0.189 ---
obs0.191 19174 93.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.96 Å2 / Biso mean: 27.451 Å2 / Biso min: 12.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2005 0 0 160 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222049
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9442779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3865250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79425.619105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.35415354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.792159
X-RAY DIFFRACTIONr_chiral_restr0.1350.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021571
X-RAY DIFFRACTIONr_nbd_refined0.2110.2891
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21389
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.212
X-RAY DIFFRACTIONr_mcbond_it0.9221.51299
X-RAY DIFFRACTIONr_mcangle_it1.3922037
X-RAY DIFFRACTIONr_scbond_it2.4743851
X-RAY DIFFRACTIONr_scangle_it3.8854.5741
LS refinement shellResolution: 1.899→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 87 -
Rwork0.21 1083 -
all-1170 -
obs--81.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1101-0.42340.10050.92470.30362.23450.0910.0176-0.2719-0.0229-0.0750.00280.35510.0925-0.0159-0.11430.017-0.0158-0.12870.018-0.094941.116417.894112.6087
210.48912.004110.718513.922910.429729.20260.31441.1830.3015-1.03470.4809-0.7368-0.73033.2231-0.79530.16980.10330.02250.75650.0090.436659.396513.534-0.5678
31.5277-0.15360.1730.80710.64811.85650.05510.0105-0.0595-0.0367-0.0133-0.04080.06820.0584-0.0418-0.0121-0.00930.0053-0.03040.01820.015640.236223.678315.0244
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A701 - 810
2X-RAY DIFFRACTION1A811 - 938
3X-RAY DIFFRACTION2P840 - 851
4X-RAY DIFFRACTION3A1 - 120

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