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- PDB-7rw8: AP2 bound to heparin in the closed conformation -

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Basic information

Entry
Database: PDB / ID: 7rw8
TitleAP2 bound to heparin in the closed conformation
Components
  • AP-2 complex subunit alpha-2
  • AP-2 complex subunit beta
  • AP-2 complex subunit mu
  • AP-2 complex subunit sigma
KeywordsENDOCYTOSIS / AP2 / clathrin vesicle / lipid-binding / adaptor / membrane / transport
Function / homology
Function and homology information


Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / clathrin adaptor complex / cardiac septum development ...Formation of annular gap junctions / Gap junction degradation / LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / VLDLR internalisation and degradation / clathrin adaptor complex / cardiac septum development / Recycling pathway of L1 / extrinsic component of presynaptic endocytic zone membrane / regulation of vesicle size / postsynaptic endocytic zone / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / membrane coat / Clathrin-mediated endocytosis / clathrin coat assembly / positive regulation of synaptic vesicle endocytosis / clathrin adaptor activity / vesicle budding from membrane / clathrin-dependent endocytosis / MHC class II antigen presentation / signal sequence binding / coronary vasculature development / positive regulation of protein localization to membrane / neurotransmitter secretion / regulation of hematopoietic stem cell differentiation / aorta development / ventricular septum development / low-density lipoprotein particle receptor binding / clathrin binding / positive regulation of endocytosis / positive regulation of receptor internalization / synaptic vesicle endocytosis / negative regulation of protein localization to plasma membrane / vesicle-mediated transport / Neutrophil degranulation / secretory granule / intracellular protein transport / kidney development / kinase binding / cytoplasmic side of plasma membrane / disordered domain specific binding / synaptic vesicle / presynapse / heart development / protein-containing complex assembly / cytoplasmic vesicle / transmembrane transporter binding / postsynapse / protein domain specific binding / synapse / lipid binding / protein kinase binding / protein-containing complex binding / glutamatergic synapse / mitochondrion
Similarity search - Function
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 ...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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
AP-2 complex subunit alpha-2 / AP-2 complex subunit sigma / AP-2 complex subunit mu / AP-2 complex subunit beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBaker, R.W. / Hollopeter, G. / Partlow, E.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM127548-01A1 United States
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structural basis of an endocytic checkpoint that primes the AP2 clathrin adaptor for cargo internalization.
Authors: Edward A Partlow / Kevin S Cannon / Gunther Hollopeter / Richard W Baker /
Abstract: Clathrin-mediated endocytosis (CME) is the main route of internalization from the plasma membrane. It is known that the heterotetrameric AP2 clathrin adaptor must open to simultaneously engage ...Clathrin-mediated endocytosis (CME) is the main route of internalization from the plasma membrane. It is known that the heterotetrameric AP2 clathrin adaptor must open to simultaneously engage membrane and endocytic cargo, yet it is unclear how transmembrane cargos are captured to catalyze CME. Using cryogenic-electron microscopy, we discover a new way in which mouse AP2 can reorganize to expose membrane- and cargo-binding pockets, which is not observed in clathrin-coated structures. Instead, it is stimulated by endocytic pioneer proteins called muniscins, which do not enter vesicles. Muniscin-engaged AP2 is primed to rearrange into the vesicle-competent conformation on binding the tyrosine cargo internalization motif (YxxΦ). We propose adaptor priming as a checkpoint to ensure cargo internalization.
History
DepositionAug 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 27, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 5, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AP-2 complex subunit alpha-2
B: AP-2 complex subunit beta
M: AP-2 complex subunit mu
S: AP-2 complex subunit sigma


Theoretical massNumber of molelcules
Total (without water)204,2924
Polymers204,2924
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, AP2 was purified by affinity and gel-filtration chromatography
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15540 Å2
ΔGint-87 kcal/mol
Surface area70900 Å2

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Components

#1: Protein AP-2 complex subunit alpha-2 / 100 kDa coated vesicle protein C / Adaptor protein complex AP-2 subunit alpha-2 / Adaptor-related ...100 kDa coated vesicle protein C / Adaptor protein complex AP-2 subunit alpha-2 / Adaptor-related protein complex 2 subunit alpha-2 / Alpha-adaptin C / Alpha2-adaptin / Clathrin assembly protein complex 2 alpha-C large chain / Plasma membrane adaptor HA2/AP2 adaptin alpha C subunit


Mass: 70573.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AP2 alpha 1-621 purified with a C-terminal GST tag / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2a2, Adtab / Plasmid: pACYC Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17427
#2: Protein AP-2 complex subunit beta / AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta ...AP105B / Adaptor protein complex AP-2 subunit beta / Adaptor-related protein complex 2 subunit beta / Beta-2-adaptin / Beta-adaptin / Clathrin assembly protein complex 2 beta large chain / Plasma membrane adaptor HA2/AP2 adaptin beta subunit


Mass: 66953.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: AP2 beta 1-591 / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2b1, Clapb1 / Plasmid: Plasmid / Details (production host): pET Duet-1 / Production host: Mus musculus (house mouse) / References: UniProt: Q9DBG3
#3: Protein AP-2 complex subunit mu / AP-2 mu chain / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit ...AP-2 mu chain / Adaptor protein complex AP-2 subunit mu / Adaptor-related protein complex 2 subunit mu / Clathrin assembly protein complex 2 mu medium chain / Clathrin coat assembly protein AP50 / Clathrin coat-associated protein AP50 / Mu2-adaptin / Plasma membrane adaptor AP-2 50 kDa protein


Mass: 49726.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2m1, Clapm1 / Plasmid: Plasmid / Details (production host): pET Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P84091
#4: Protein AP-2 complex subunit sigma / Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / ...Adaptor protein complex AP-2 subunit sigma / Adaptor-related protein complex 2 subunit sigma / Clathrin assembly protein 2 sigma small chain / Clathrin coat assembly protein AP17 / Clathrin coat-associated protein AP17 / Plasma membrane adaptor AP-2 17 kDa protein / Sigma-adaptin 3b / Sigma2-adaptin


Mass: 17038.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ap2s1, Ap17, Claps2 / Plasmid: Plasmid / Details (production host): pACYC Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P62743

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: AP2 complex bound to heparin / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pACYC Duet; pET Duet
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2150 mMSodium ChlorideNaCl1
30.05 %n-octyl-beta-d-glucosideC14H28O61
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Heparin added at a 2-fold excess 20 mM HEPES pH 7.4, 150 mM NaCl, 1 mM DTT, 0.05% beta-OG
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blot force -10, 4 second blot, 4 uL sample

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARC3.2.0particle selection
2SerialEMimage acquisition
4cryoSPARC3.2.0CTF correction
7Coot0.8.9.1model fitting
8UCSF Chimera1.14model fitting
11cryoSPARC3.2.0final Euler assignment
13cryoSPARC3.2.03D reconstruction
14PHENIX1.19.2model refinement
Image processingDetails: Counting Mode
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 805304
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157670 / Details: Non-Uniform refinement in cryoSPARC v3.2.0 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Details: phenix.real_space_refine
Atomic model buildingPDB-ID: 2VGL

2vgl


Accession code: 2VGL / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412808
ELECTRON MICROSCOPYf_angle_d0.53717509
ELECTRON MICROSCOPYf_dihedral_angle_d3.9761823
ELECTRON MICROSCOPYf_chiral_restr0.0412170
ELECTRON MICROSCOPYf_plane_restr0.0042207

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