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- PDB-3hs9: Intersectin 1-peptide-AP2 beta ear complex -

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Basic information

Entry
Database: PDB / ID: 3hs9
TitleIntersectin 1-peptide-AP2 beta ear complex
Components
  • AP-2 complex subunit beta-1
  • peptide from Intersectin-1, residues 841-851
KeywordsENDOCYTOSIS / clathrin / adaptor complex AP-2 / Alternative splicing / Cell membrane / Coated pit / Membrane / Disease mutation / Transferase
Function / homology
Function and homology information


: / AP-type membrane coat adaptor complex / NRAGE signals death through JNK / presynaptic endocytic zone / RHOQ GTPase cycle / G alpha (12/13) signalling events / positive regulation of caveolin-mediated endocytosis / clathrin-dependent synaptic vesicle endocytosis / CDC42 GTPase cycle / protein localization => GO:0008104 ...: / AP-type membrane coat adaptor complex / NRAGE signals death through JNK / presynaptic endocytic zone / RHOQ GTPase cycle / G alpha (12/13) signalling events / positive regulation of caveolin-mediated endocytosis / clathrin-dependent synaptic vesicle endocytosis / CDC42 GTPase cycle / protein localization => GO:0008104 / EPHB-mediated forward signaling / NRAGE signals death through JNK / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / VLDLR internalisation and degradation / Retrograde neurotrophin signalling / RHOG GTPase cycle / clathrin coat / clathrin adaptor complex / WNT5A-dependent internalization of FZD4 / extrinsic component of presynaptic endocytic zone membrane / cardiac septum development / G alpha (12/13) signalling events / MHC class II antigen presentation / AP-2 adaptor complex / positive regulation of growth hormone secretion / postsynaptic neurotransmitter receptor internalization / Recycling pathway of L1 / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / postsynaptic actin cytoskeleton / Cargo recognition for clathrin-mediated endocytosis / EPHB-mediated forward signaling / regulation of modification of postsynaptic actin cytoskeleton / Clathrin-mediated endocytosis / Clathrin-mediated endocytosis / apical dendrite / clathrin-dependent endocytosis / neurotransmitter receptor internalization / positive regulation of protein localization to membrane / kinase activator activity / coronary vasculature development / proline-rich region binding / aorta development / regulation of postsynapse organization / positive regulation of dendritic spine development / ventricular septum development / endosomal transport / clathrin binding / small GTPase-mediated signal transduction / intracellular vesicle / positive regulation of endocytosis / exocytosis / Trafficking of GluR2-containing AMPA receptors / calyx of Held / synaptic vesicle endocytosis / endocytic vesicle / clathrin-coated pit / vesicle-mediated transport / guanyl-nucleotide exchange factor activity / kidney development / intracellular protein transport / brain development / protein localization / terminal bouton / recycling endosome / endocytosis / protein transport / lamellipodium / presynaptic membrane / nuclear envelope / heart development / postsynapse / neuron apoptotic process / negative regulation of neuron apoptotic process / dendritic spine / molecular adaptor activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / neuronal cell body / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Immunoglobulin-like - #1150 / Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / TATA-Binding Protein / Clathrin adaptor, beta-adaptin, appendage, Ig-like subdomain ...Immunoglobulin-like - #1150 / Intersectin-1, AP2 binding region / Intersectin and clathrin adaptor AP2 binding region / Pleckstrin homology domain / 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 / 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 / Variant SH3 domain / TATA-Binding Protein / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / Armadillo/beta-catenin-like repeats / Armadillo / 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 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / 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 beta / Intersectin-1 / Intersectin-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: AP-2 complex subunit beta-1
P: peptide from Intersectin-1, residues 841-851


Theoretical massNumber of molelcules
Total (without water)30,6682
Polymers30,6682
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-5 kcal/mol
Surface area12630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.088, 47.103, 58.945
Angle α, β, γ (deg.)90.000, 97.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AP-2 complex subunit beta-1 / Adapter-related protein complex 2 beta-1 subunit / Beta2-adaptin / Beta-adaptin / Plasma membrane ...Adapter-related protein complex 2 beta-1 subunit / Beta2-adaptin / Beta-adaptin / Plasma membrane adaptor HA2/AP2 adaptin beta subunit / Clathrin assembly protein complex 2 beta large chain / AP105B


Mass: 29246.605 Da / Num. of mol.: 1 / Fragment: UNP residues 701-937
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ap2b1, Clapb1 / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62944
#2: Protein/peptide peptide from Intersectin-1, residues 841-851 /


Mass: 1421.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q9Z0R4, UniProt: Q9WVE9*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG8000, 100mM HEPES, 4mM DTT, pH 7.5, 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: May 25, 2008 / 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: 1.95→60.523 Å / Num. obs: 23441 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 9.119
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-2.063.80.4661.61297434240.46696.3
2.06-2.183.80.2622.91220032150.26296.4
2.18-2.333.80.2043.41142530300.20496.7
2.33-2.523.80.1116.61076128490.11197.1
2.52-2.763.80.0719.4984826090.07197.2
2.76-3.083.80.04612.9903123880.04697.4
3.08-3.563.70.03615789621090.03697.5
3.56-4.363.70.03515.9666317900.03597.4
4.36-6.173.70.03117.5505313760.03196.5
6.17-58.423.50.03119.922626510.03181.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G30

2g30


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.312 / WRfactor Rwork: 0.27 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.642 / SU B: 11.424 / SU ML: 0.259 / SU R Cruickshank DPI: 0.275 / SU Rfree: 0.221 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.283 743 4.2 %RANDOM
Rwork0.249 ---
obs0.251 17529 95.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.72 Å2 / Biso mean: 53.732 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--4.95 Å20 Å2-0.17 Å2
2--8.2 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 133 2085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222000
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9512722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9265242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.84525.69993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.833155
X-RAY DIFFRACTIONr_chiral_restr0.0910.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021518
X-RAY DIFFRACTIONr_nbd_refined0.2320.2919
X-RAY DIFFRACTIONr_nbtor_refined0.3140.21331
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.29
X-RAY DIFFRACTIONr_mcbond_it0.8121.51261
X-RAY DIFFRACTIONr_mcangle_it1.40421992
X-RAY DIFFRACTIONr_scbond_it1.653834
X-RAY DIFFRACTIONr_scangle_it2.6284.5730
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 42 -
Rwork0.409 1245 -
all-1287 -
obs--96.48 %

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