[English] 日本語
Yorodumi
- EMDB-12224: Vps26 dimer region of the fungal membrane-assembled retromer:Grd1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-12224
TitleVps26 dimer region of the fungal membrane-assembled retromer:Grd19 complex.
Map dataSharpened, locally filtered map of VPS26 dimer region of the fungal retromer:Grd19 complex assembled on the membrane
Sample
  • Complex: Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 cargo-containing complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
    • Protein or peptide: Sorting nexin-3
    • Protein or peptide: Vacuolar protein sorting-associated protein 26-like protein
    • Protein or peptide: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.
  • Ligand: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
Keywordsendosomes / coat proteins / membrane trafficking / cargo-sorting / ENDOCYTOSIS
Function / homology
Function and homology information


vanadium ion transmembrane transporter activity / vanadium ion transport / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / nickel cation transmembrane transporter activity / transition metal ion transmembrane transporter activity / late endosome to Golgi transport / solute:proton symporter activity ...vanadium ion transmembrane transporter activity / vanadium ion transport / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / lead ion transport / nickel cation transmembrane transporter activity / transition metal ion transmembrane transporter activity / late endosome to Golgi transport / solute:proton symporter activity / inorganic cation transmembrane transporter activity / cadmium ion transmembrane transport / Metal ion SLC transporters / manganese ion transport / nickel cation transport / detection of oxygen / retromer, cargo-selective complex / cadmium ion transmembrane transporter activity / manganese ion transmembrane transporter activity / iron import into cell / copper ion transmembrane transporter activity / cobalt ion transport / cobalt ion transmembrane transporter activity / retromer complex binding / ferrous iron transmembrane transporter activity / iron ion transmembrane transporter activity / retromer complex / zinc ion transmembrane transporter activity / iron ion transmembrane transport / copper ion transport / basal part of cell / endocytic recycling / phosphatidylinositol-3-phosphate binding / vacuole / retrograde transport, endosome to Golgi / response to iron ion / heme biosynthetic process / dendrite morphogenesis / cadmium ion binding / erythrocyte development / intracellular protein transport / trans-Golgi network / Iron uptake and transport / brush border membrane / recycling endosome / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / late endosome membrane / apical part of cell / late endosome / protein transport / extracellular vesicle / iron ion transport / cellular response to oxidative stress / early endosome membrane / cytoplasmic vesicle / mitochondrial outer membrane / intracellular iron ion homeostasis / learning or memory / early endosome / response to hypoxia / lysosome / endosome membrane / apical plasma membrane / Golgi membrane / lysosomal membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / mitochondrion / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fungal SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / NRAMP family / Natural resistance-associated macrophage protein-like / PhoX homologous domain, present in p47phox and p40phox. ...Fungal SNX3, PX domain / : / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / NRAMP family / Natural resistance-associated macrophage protein-like / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / Arrestin-like, C-terminal
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 26-like protein / Sorting nexin-3 / Vacuolar protein sorting-associated protein 35 / Natural resistance-associated macrophage protein 2
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 9.2 Å
AuthorsLeneva N / Kovtun O
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Wellcome Trust207455/Z/17/Z United Kingdom
Wellcome Trust206171/Z/17/Z United Kingdom
Wellcome Trust202905/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSION United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly.
Authors: Natalya Leneva / Oleksiy Kovtun / Dustin R Morado / John A G Briggs / David J Owen /
Abstract: Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core ...Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes.
History
DepositionJan 18, 2021-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.235
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.235
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7blq
  • Surface level: 0.235
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12224.png

Downloads & links

-
Map

FileDownload / File: emd_12224.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, locally filtered map of VPS26 dimer region of the fungal retromer:Grd19 complex assembled on the membrane
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 100 pix.
= 275.8 Å		2.76 Å/pix.
x 100 pix.
= 275.8 Å		2.76 Å/pix.
x 100 pix.
= 275.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.758 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.235 / Movie #1: 0.235
Minimum - Maximum-0.5964883 - 1.1464814
Average (Standard dev.)0.0036801388 (±0.063661784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 275.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.7582.7582.758
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z275.800275.800275.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.5961.1460.004

-
Supplemental data

-
Mask #1

Fileemd_12224_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map2

Fileemd_12224_half_map_1.map
Annotationhalf-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-map1

Fileemd_12224_half_map_2.map
Annotationhalf-map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Vps26 dimer region of the fungal membrane-assembled retromer:Grd1...

EntireName: Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 cargo-containing complex
Components
  • Complex: Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 cargo-containing complex
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
    • Protein or peptide: Sorting nexin-3
    • Protein or peptide: Vacuolar protein sorting-associated protein 26-like protein
    • Protein or peptide: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.
  • Ligand: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE

-
Supramolecule #1: Vps26 dimer region of the fungal membrane-assembled retromer:Grd1...

SupramoleculeName: Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 cargo-containing complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: fungal retromer:Grd19 complex assembled on liposomes containing Kex2 cargo peptide.
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

-
Macromolecule #1: Vacuolar protein sorting-associated protein 35

MacromoleculeName: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 34.014195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RLLEDALIAV RQQTAMMRKF LDTPGKLMDA LKCCSTLVSE LRTSSLSPKQ YYELYMAVFD ALRYLSAHLR ENHPVNHLAD LYELVQYAG NIIPRLYLMI TVGTAYMSID GAPVKELMKD MMDMSRGVQH PVRGLFLRYY LSGQARDYLP TGDSDGPEGN L QDSINFIL ...String:
RLLEDALIAV RQQTAMMRKF LDTPGKLMDA LKCCSTLVSE LRTSSLSPKQ YYELYMAVFD ALRYLSAHLR ENHPVNHLAD LYELVQYAG NIIPRLYLMI TVGTAYMSID GAPVKELMKD MMDMSRGVQH PVRGLFLRYY LSGQARDYLP TGDSDGPEGN L QDSINFIL TNFVEMNKLW VRLQHQGHSR ERDLRTQERR ELQLLVGSNI VRLSQLVDLP TYRDSILGPL LEQIVQCRDI LA QEYLLEV ITQVFPDEYH LHTLDQFLGA VSRLNPHVNV KAIVIGMMNR LSDYAERE

UniProtKB: Vacuolar protein sorting-associated protein 35

-
Macromolecule #2: Sorting nexin-3

MacromoleculeName: Sorting nexin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 13.52549 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PPENFLEIEV RNPQTHGVGR HMYTDYEIVC RTNIPAFKLR QSSVRRRYSD FEYFRDILER ESARVTIPPL PGKVFTNRFS DEVIENRRA GLEKFLKIVV GHPLLQTGSK VLAAFVQ

UniProtKB: Sorting nexin-3

-
Macromolecule #3: Vacuolar protein sorting-associated protein 26-like protein

MacromoleculeName: Vacuolar protein sorting-associated protein 26-like protein
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 34.308449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FSTPVDIDIV LADADKRAMV DVKLDKNRRE KVPLYMDGES VKGCVTVRPK DGKRLEHTGI KVQFIGTIEM FFDRGNHYEF LSLVQELAA PGELQHPQTF DFNFKNVEKQ YESYNGINVK LRYFVRVTVS RRMADVIREK DIWVYSYRIP PELNSSIKMD V GIEDCLHI ...String:
FSTPVDIDIV LADADKRAMV DVKLDKNRRE KVPLYMDGES VKGCVTVRPK DGKRLEHTGI KVQFIGTIEM FFDRGNHYEF LSLVQELAA PGELQHPQTF DFNFKNVEKQ YESYNGINVK LRYFVRVTVS RRMADVIREK DIWVYSYRIP PELNSSIKMD V GIEDCLHI EFEYSKSKYH LKDVIVGRIY FLLVRLKIKH MELSIIRRET TGVAPNQYNE SETLVRFEIM DGSPSRGETI PI RLFLGGF DLTPTFRDVN KKFSTRYYLS LVLIDEDARR YFKQSEIILY RQPPE

UniProtKB: Vacuolar protein sorting-associated protein 26-like protein

-
Macromolecule #4: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sor...

MacromoleculeName: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo.
type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Molecular weightTheoretical: 1.221422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QPELYLLNTM

-
Macromolecule #5: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOX...

MacromoleculeName: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE
type: ligand / ID: 5 / Number of copies: 2 / Formula: PIB
Molecular weightTheoretical: 554.374 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 49886
ExtractionNumber tomograms: 82 / Number images used: 449807
Final angle assignmentType: OTHER
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