+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11987 | |||||||||
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Title | Structure of the endocytic adaptor complex AENTH | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Membrane protein / clathrin-mediated endocytosis / adapter protein / Sla2 / Epsin-1 / ENTH / ANTH / CELL ADHESION | |||||||||
Function / homology | Function and homology information Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / clathrin light chain binding / incipient cellular bud site / negative regulation of Arp2/3 complex-mediated actin nucleation / cellular bud tip / clathrin coat assembly / actin cortical patch / clathrin adaptor activity ...Cargo recognition for clathrin-mediated endocytosis / actin cortical patch assembly / clathrin vesicle coat / clathrin light chain binding / incipient cellular bud site / negative regulation of Arp2/3 complex-mediated actin nucleation / cellular bud tip / clathrin coat assembly / actin cortical patch / clathrin adaptor activity / cellular bud neck / mating projection tip / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / clathrin-coated vesicle / clathrin binding / K63-linked polyubiquitin modification-dependent protein binding / cortical actin cytoskeleton / actin filament organization / ubiquitin binding / phospholipid binding / endocytosis / actin filament binding / early endosome / endosome / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Klebl DP / Lizarrondo J | |||||||||
Funding support | Germany, United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure of the endocytic adaptor complex reveals the basis for efficient membrane anchoring during clathrin-mediated endocytosis. Authors: Javier Lizarrondo / David P Klebl / Stephan Niebling / Marc Abella / Martin A Schroer / Haydyn D T Mertens / Katharina Veith / Roland Thuenauer / Dmitri I Svergun / Michal Skruzny / Frank ...Authors: Javier Lizarrondo / David P Klebl / Stephan Niebling / Marc Abella / Martin A Schroer / Haydyn D T Mertens / Katharina Veith / Roland Thuenauer / Dmitri I Svergun / Michal Skruzny / Frank Sobott / Stephen P Muench / Maria M Garcia-Alai / Abstract: During clathrin-mediated endocytosis, a complex and dynamic network of protein-membrane interactions cooperate to achieve membrane invagination. Throughout this process in yeast, endocytic coat ...During clathrin-mediated endocytosis, a complex and dynamic network of protein-membrane interactions cooperate to achieve membrane invagination. Throughout this process in yeast, endocytic coat adaptors, Sla2 and Ent1, must remain attached to the plasma membrane to transmit force from the actin cytoskeleton required for successful membrane invagination. Here, we present a cryo-EM structure of a 16-mer complex of the ANTH and ENTH membrane-binding domains from Sla2 and Ent1 bound to PIP that constitutes the anchor to the plasma membrane. Detailed in vitro and in vivo mutagenesis of the complex interfaces delineate the key interactions for complex formation and deficient cell growth phenotypes demonstrate its biological relevance. A hetero-tetrameric unit binds PIP molecules at the ANTH-ENTH interfaces and can form larger assemblies to contribute to membrane remodeling. Finally, a time-resolved small-angle X-ray scattering study of the interaction of these adaptor domains in vitro suggests that ANTH and ENTH domains have evolved to achieve a fast subsecond timescale assembly in the presence of PIP and do not require further proteins to form a stable complex. Together, these findings provide a molecular understanding of an essential piece in the molecular puzzle of clathrin-coated endocytic sites. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11987.map.gz | 5.8 MB | EMDB map data format | |
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Header (meta data) | emd-11987-v30.xml emd-11987.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11987_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_11987.png | 139 KB | ||
Masks | emd_11987_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-11987.cif.gz | 6 KB | ||
Others | emd_11987_half_map_1.map.gz emd_11987_half_map_2.map.gz | 48.7 MB 48.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11987 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11987 | HTTPS FTP |
-Validation report
Summary document | emd_11987_validation.pdf.gz | 797.4 KB | Display | EMDB validaton report |
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Full document | emd_11987_full_validation.pdf.gz | 796.9 KB | Display | |
Data in XML | emd_11987_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | emd_11987_validation.cif.gz | 20.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11987 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11987 | HTTPS FTP |
-Related structure data
Related structure data | 7b2lMC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11987.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11987_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11987_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11987_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : 16 mer of 8 Sla2 ANTH and 8 Epsin-1 ENTH domains in complex with PIP2
Entire | Name: 16 mer of 8 Sla2 ANTH and 8 Epsin-1 ENTH domains in complex with PIP2 |
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Components |
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-Supramolecule #1: 16 mer of 8 Sla2 ANTH and 8 Epsin-1 ENTH domains in complex with PIP2
Supramolecule | Name: 16 mer of 8 Sla2 ANTH and 8 Epsin-1 ENTH domains in complex with PIP2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
-Macromolecule #1: ENTH domain of epsin Ent1
Macromolecule | Name: ENTH domain of epsin Ent1 / type: protein_or_peptide / ID: 1 / Details: ENTH domain of epsin Ent1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 18.88051 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GAMGSMSKQF VRSAKNLVKG YSSTQVLVRN ATSNDNHQVS KDSLIELAEK SYDSADFFEI MDMLDKRLND KGKYWRHIAK ALTVIDYLI RFGSENCVLW CRENLYIIKT LKEFRHEDDE GIDQGQIVRV KAKELTALLS DDERLNEERN MNIKGRNRKG R RR UniProtKB: Epsin-1 |
-Macromolecule #2: ANTH domain of Sla2
Macromolecule | Name: ANTH domain of Sla2 / type: protein_or_peptide / ID: 2 / Details: ANTH domain of Sla2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) |
Molecular weight | Theoretical: 33.257004 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: GAMGSMSRID SDLQKALKKA CSVEETAPKR KHVRACIVYT WDHQSSKAVF TTLKTLPLAN DEVQLFKMLI VLHKIIQEGH PSALAEAIR DRDWIRSLGR VHSGGSSYSK LIREYVRYLV LKLDFHAHHR GFNNGTFEYE EYVSLVSVSD PDEGYETILD L MSLQDSLD ...String: GAMGSMSRID SDLQKALKKA CSVEETAPKR KHVRACIVYT WDHQSSKAVF TTLKTLPLAN DEVQLFKMLI VLHKIIQEGH PSALAEAIR DRDWIRSLGR VHSGGSSYSK LIREYVRYLV LKLDFHAHHR GFNNGTFEYE EYVSLVSVSD PDEGYETILD L MSLQDSLD EFSQIIFASI QSERRNTECK ISALIPLIAE SYGIYKFITS MLRAMHRQLN DAEGDAALQP LKERYELQHA RL FEFYADC SSVKYLTTLV TIPKLPVDAP DVFLINDVDE SKEIKFKKRE PSVT UniProtKB: Protein SLA2 |
-Macromolecule #3: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...
Macromolecule | Name: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate type: ligand / ID: 3 / Number of copies: 20 / Formula: PIO |
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Molecular weight | Theoretical: 746.566 Da |
Chemical component information | ChemComp-PIO: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
Details | 20 mM Tris, 250 mM NaCl and 1 mM DTT |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 75.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |