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- PDB-8afz: Architecture of the ESCPE-1 membrane coat -

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Basic information

Entry
Database: PDB / ID: 8afz
TitleArchitecture of the ESCPE-1 membrane coat
Components
  • Cation-independent mannose-6-phosphate receptor
  • Sorting nexin-1
  • Sorting nexin-5
KeywordsTRANSPORT PROTEIN / sorting nexins / PX domain / BAR domain / endosomes / retrograde transport / endocytic recycling / cargo recognition / protein coat / membrane recruitment / membrane deformation / membrane tubules.
Function / homology
Function and homology information


retromer, tubulation complex / lamellipodium morphogenesis / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network ...retromer, tubulation complex / lamellipodium morphogenesis / epidermal growth factor catabolic process / pinocytosis / cytoplasmic side of early endosome membrane / leptin receptor binding / tubular endosome / macropinocytic cup / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / clathrin coat / retromer complex binding / insulin-like growth factor receptor activity / response to tetrachloromethane / insulin-like growth factor binding / retromer complex / transferrin receptor binding / phosphatidylinositol-5-phosphate binding / insulin-like growth factor II binding / trans-Golgi network transport vesicle / positive regulation by host of viral process / retinoic acid binding / retrograde transport, endosome to Golgi / phosphatidylinositol-4-phosphate binding / lysosomal transport / phosphatidylinositol-3,5-bisphosphate binding / epidermal growth factor receptor binding / Golgi Associated Vesicle Biogenesis / nuclear envelope lumen / brush border / D-mannose binding / dynactin binding / phagocytic cup / endocytic vesicle / G-protein alpha-subunit binding / D1 dopamine receptor binding / animal organ regeneration / regulation of macroautophagy / response to retinoic acid / positive regulation of insulin receptor signaling pathway / transport vesicle / ruffle / negative regulation of blood pressure / post-embryonic development / receptor-mediated endocytosis / phosphatidylinositol binding / liver development / secretory granule membrane / trans-Golgi network membrane / phosphoprotein binding / intracellular protein transport / insulin receptor binding / clathrin-coated endocytic vesicle membrane / trans-Golgi network / receptor internalization / cytoplasmic side of plasma membrane / late endosome / Cargo recognition for clathrin-mediated endocytosis / lamellipodium / Clathrin-mediated endocytosis / signaling receptor activity / early endosome membrane / spermatogenesis / vesicle / lysosome / early endosome / endosome membrane / endosome / cadherin binding / positive regulation of apoptotic process / protein heterodimerization activity / G protein-coupled receptor signaling pathway / Golgi membrane / intracellular membrane-bounded organelle / focal adhesion / Neutrophil degranulation / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / cell surface / signal transduction / protein homodimerization activity / protein-containing complex / extracellular exosome / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Cation-independent mannose-6-phosphate receptor repeat ...Sorting nexin, N-terminal / Sorting nexin-1 / Sorting Nexin 1, PX domain / Sorting nexin, N-terminal domain / SNX5, PX domain / Sorting nexin-5 / Sorting nexin-5/6/32 / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Cation-independent mannose-6-phosphate receptor repeat / Mannose-6-phosphate receptor binding domain superfamily / MRH domain / MRH domain profile. / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / AH/BAR domain superfamily / Kringle-like fold
Similarity search - Domain/homology
Cation-independent mannose-6-phosphate receptor / Sorting nexin-1 / Sorting nexin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 10 Å
AuthorsLopez-Robles, C. / Scaramuzza, S. / Astorga-Simon, E. / Ishida, M. / Williamsom, C.D. / Banos-Mateos, S. / Gil-Carton, D. / Romero, M. / Vidaurrazaga, A. / Fernandez-Recio, J. ...Lopez-Robles, C. / Scaramuzza, S. / Astorga-Simon, E. / Ishida, M. / Williamsom, C.D. / Banos-Mateos, S. / Gil-Carton, D. / Romero, M. / Vidaurrazaga, A. / Fernandez-Recio, J. / Rojas, A.L. / Bonifacino, J.S. / Castano-Diez, D. / Hierro, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-119132GB-100 Spain
CitationJournal: Nat Struct Mol Biol / Year: 2023
Title: Architecture of the ESCPE-1 membrane coat.
Authors: Carlos Lopez-Robles / Stefano Scaramuzza / Elsa N Astorga-Simon / Morié Ishida / Chad D Williamson / Soledad Baños-Mateos / David Gil-Carton / Miguel Romero-Durana / Ander Vidaurrazaga / ...Authors: Carlos Lopez-Robles / Stefano Scaramuzza / Elsa N Astorga-Simon / Morié Ishida / Chad D Williamson / Soledad Baños-Mateos / David Gil-Carton / Miguel Romero-Durana / Ander Vidaurrazaga / Juan Fernandez-Recio / Adriana L Rojas / Juan S Bonifacino / Daniel Castaño-Díez / Aitor Hierro /
Abstract: Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1) ...Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.
History
DepositionJul 18, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 2.0Jun 28, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / citation_author / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_torsion / struct_sheet_range
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Atomic clashes / Provider: author / Type: Coordinate replacement
Revision 2.1Jul 26, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.2Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sorting nexin-1
B: Sorting nexin-5
C: Cation-independent mannose-6-phosphate receptor


Theoretical massNumber of molelcules
Total (without water)109,8023
Polymers109,8023
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sorting nexin-1


Mass: 59144.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13596
#2: Protein Sorting nexin-5


Mass: 46891.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5X3
#3: Protein/peptide Cation-independent mannose-6-phosphate receptor / CI Man-6-P receptor / CI-MPR / M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like ...CI Man-6-P receptor / CI-MPR / M6PR / 300 kDa mannose 6-phosphate receptor / MPR 300 / Insulin-like growth factor 2 receptor / Insulin-like growth factor II receptor / IGF-II receptor / M6P/IGF2 receptor / M6P/IGF2R


Mass: 3766.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGF2R, MPRI / Production host: Escherichia coli (E. coli) / References: UniProt: P11717

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Endosomal Sorting Complex for Promoting Exit 1 (ESCPE-1)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.110 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 282 K / Details: Incubation time 30s Blotting time 2s

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.8 e/Å2 / Avg electron dose per subtomogram: 114 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 10

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Processing

CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 10 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15116 / Algorithm: BACK PROJECTION / Symmetry type: POINT
EM volume selectionNum. of tomograms: 57 / Num. of volumes extracted: 77436

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