[English] 日本語
Yorodumi
- EMDB-15413: Architecture of the ESCPE-1 membrane coat -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15413
TitleArchitecture of the ESCPE-1 membrane coat
Map data
Sample
  • Complex: Endosomal Sorting Complex for Promoting Exit 1 (ESCPE-1)
    • Protein or peptide: Sorting nexin-1
    • Protein or peptide: Sorting nexin-5
    • Protein or peptide: Cation-independent mannose-6-phosphate receptor
Keywordssorting nexins / PX domain / BAR domain / endosomes / retrograde transport / endocytic recycling / cargo recognition / protein coat / membrane recruitment / membrane deformation / membrane tubules. / TRANSPORT PROTEIN
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)
Methodsubtomogram averaging / cryo EM / Resolution: 10.0 Å
AuthorsLopez-Robles C / Scaramuzza S / Astorga-Simon E / Ishida M / Williamsom CD / Banos-Mateos S / Gil-Carton D / Romero M / Vidaurrazaga A / Fernandez-Recio J ...Lopez-Robles C / Scaramuzza S / Astorga-Simon E / Ishida M / Williamsom CD / Banos-Mateos S / Gil-Carton D / Romero M / Vidaurrazaga A / Fernandez-Recio J / Rojas AL / Bonifacino JS / Castano-Diez D / Hierro A
Funding support Spain, 1 items
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, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15413.png

Downloads & links

-
Map

FileDownload / File: emd_15413.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.73 Å/pix.
x 96 pix.
= 262.08 Å		2.73 Å/pix.
x 96 pix.
= 262.08 Å		2.73 Å/pix.
x 96 pix.
= 262.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-8.233516 - 7.2678957
Average (Standard dev.)-0.030197147 (±0.63029784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 262.08002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_15413_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_15413_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Endosomal Sorting Complex for Promoting Exit 1 (ESCPE-1)

EntireName: Endosomal Sorting Complex for Promoting Exit 1 (ESCPE-1)
Components
  • Complex: Endosomal Sorting Complex for Promoting Exit 1 (ESCPE-1)
    • Protein or peptide: Sorting nexin-1
    • Protein or peptide: Sorting nexin-5
    • Protein or peptide: Cation-independent mannose-6-phosphate receptor

-
Supramolecule #1: Endosomal Sorting Complex for Promoting Exit 1 (ESCPE-1)

SupramoleculeName: Endosomal Sorting Complex for Promoting Exit 1 (ESCPE-1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 110 KDa

-
Macromolecule #1: Sorting nexin-1

MacromoleculeName: Sorting nexin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.14434 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASGGGGCSA SERLPPPFPG LEPESEGAAG GSEPEAGDSD TEGEDIFTGA AVVSKHQSPK ITTSLLPINN GSKENGIHEE QDQEPQDLF ADATVELSLD STQNNQKKVL AKTLISLPPQ EATNSSKPQP TYEELEEEEQ EDQFDLTVGI TDPEKIGDGM N AYVAYKVT ...String:
MASGGGGCSA SERLPPPFPG LEPESEGAAG GSEPEAGDSD TEGEDIFTGA AVVSKHQSPK ITTSLLPINN GSKENGIHEE QDQEPQDLF ADATVELSLD STQNNQKKVL AKTLISLPPQ EATNSSKPQP TYEELEEEEQ EDQFDLTVGI TDPEKIGDGM N AYVAYKVT TQTSLPLFRS KQFAVKRRFS DFLGLYEKLS EKHSQNGFIV PPPPEKSLIG MTKVKVGKED SSSAEFLEKR RA ALERYLQ RIVNHPTMLQ DPDVREFLEK EELPRAVGTQ TLSGAGLLKM FNKATDAVSK MTIKMNESDI WFEEKLQEVE CEE QRLRKL HAVVETLVNH RKELALNTAQ FAKSLAMLGS SEDNTALSRA LSQLAEVEEK IEQLHQEQAN NDFFLLAELL SDYI RLLAI VRAAFDQRMK TWQRWQDAQA TLQKKREAEA RLLWANKPDK LQQAKDEILE WESRVTQYER DFERISTVVR KEVIR FEKE KSKDFKNHVI KYLETLLYSQ QQLAKYWEAF LPEAKAIS

UniProtKB: Sorting nexin-1

-
Macromolecule #2: Sorting nexin-5

MacromoleculeName: Sorting nexin-5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.891504 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAVPELLQQ QEEDRSKLRS VSVDLNVDPS LQIDIPDALS ERDKVKFTVH TKTTLPTFQS PEFSVTRQHE DFVWLHDTLI ETTDYAGLI IPPAPTKPDF DGPREKMQKL GEGEGSMTKE EFAKMKQELE AEYLAVFKKT VSSHEVFLQR LSSHPVLSKD R NFHVFLEY ...String:
MAAVPELLQQ QEEDRSKLRS VSVDLNVDPS LQIDIPDALS ERDKVKFTVH TKTTLPTFQS PEFSVTRQHE DFVWLHDTLI ETTDYAGLI IPPAPTKPDF DGPREKMQKL GEGEGSMTKE EFAKMKQELE AEYLAVFKKT VSSHEVFLQR LSSHPVLSKD R NFHVFLEY DQDLSVRRKN TKEMFGGFFK SVVKSADEVL FTGVKEVDDF FEQEKNFLIN YYNRIKDSCV KADKMTRSHK NV ADDYIHT AACLHSLALE EPTVIKKYLL KVAELFEKLR KVEGRVSSDE DLKLTELLRY YMLNIEAAKD LLYRRTKALI DYE NSNKAL DKARLKSKDV KLAEAHQQEC CQKFEQLSES AKEELINFKR KRVAAFRKNL IEMSELEIKH ARNNVSLLQS CIDL FKNN

UniProtKB: Sorting nexin-5

-
Macromolecule #3: Cation-independent mannose-6-phosphate receptor

MacromoleculeName: Cation-independent mannose-6-phosphate receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.766033 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNVSYKYSKV NKEEETDENE TEWLMEEIQL P

UniProtKB: Cation-independent mannose-6-phosphate receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK II / Details: Incubation time 30s Blotting time 2s.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 2.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 15116
ExtractionNumber tomograms: 57 / Number images used: 77436
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more