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- EMDB-12226: Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12226 | ||||||||||||||||||
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Title | Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-BAR) complex. | ||||||||||||||||||
![]() | LAFTER-filtered map of Vps35/Vps29 arch of fungal retromer:Vps5 assembled on the membrane | ||||||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||
Method | subtomogram averaging / ![]() | ||||||||||||||||||
![]() | Leneva N / Kovtun O / Morado DR / Briggs JAG / Owen DJ | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 4.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 3.8 KB | Display | ![]() |
Images | ![]() | 93.7 KB | ||
Masks | ![]() | 4.3 MB | ![]() | |
Filedesc metadata | ![]() | 6 KB | ||
Others | ![]() ![]() | 4.1 MB 4.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7blrMC ![]() 7blnC ![]() 7bloC ![]() 7blpC ![]() 7blqC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | LAFTER-filtered map of Vps35/Vps29 arch of fungal retromer:Vps5 assembled on the membrane | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: half-map2
File | emd_12226_half_map_1.map | ||||||||||||
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Annotation | half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map1
File | emd_12226_half_map_2.map | ||||||||||||
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Annotation | half-map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex.
Entire | Name: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex. |
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Components |
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-Supramolecule #1: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex.
Supramolecule | Name: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: fungal retromer:Vps5 complex assembled on liposomes. |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Vacuolar protein sorting-associated protein 35
Macromolecule | Name: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 98.566781 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MSTPAPPEEQ ARLLEDALIA VRQQTAMMRK FLDTPGKLMD ALKCCSTLVS ELRTSSLSPK QYYELYMAVF DALRYLSAHL RENHPVNHL ADLYELVQYA GNIIPRLYLM ITVGTAYMSI DGAPVKELMK DMMDMSRGVQ HPVRGLFLRY YLSGQARDYL P TGDSDGPE ...String: MSTPAPPEEQ ARLLEDALIA VRQQTAMMRK FLDTPGKLMD ALKCCSTLVS ELRTSSLSPK QYYELYMAVF DALRYLSAHL RENHPVNHL ADLYELVQYA GNIIPRLYLM ITVGTAYMSI DGAPVKELMK DMMDMSRGVQ HPVRGLFLRY YLSGQARDYL P TGDSDGPE GNLQDSINFI LTNFVEMNKL WVRLQHQGHS RERDLRTQER RELQLLVGSN IVRLSQLVDL PTYRDSILGP LL EQIVQCR DILAQEYLLE VITQVFPDEY HLHTLDQFLG AVSRLNPHVN VKAIVIGMMN RLSDYAERES QNEPEEDRAK LEE EALAKL LEKTKLGQNS ELEPQNGDHP DTEVSSTTDS AQAPSTADSD TTAVNGEEEP VRKRRGIPVN VPLYDIFFDQ VQHL VQAQH LPIQDTIALC CSLANLSLNI YPERLDYVDG ILAYALAKVK EHANSADLHS QPAQQSLLSL LQSPLRRYVS IFTAL SLPT YVSLFQAQTY PTRRAIAGEI VRTLLKNQTL ISTPAHLENV LEILKVLIKE GSQPPAGYPG VVQPRARPLE TDETME EQG WLARLVHLIH SDDNDTQFRL LQMTRKAYAE GNERIRTTTP PLITAGLKLA RRFKAREHYD DNWSSQSSSL FKFLHSA IS TLYTRVNGPG VADLCLRLFC SCGQVADMTE FEEVAYEFFA QAFTVYEESI SDSKAQFQAV CVIASALHRT RNFGRENY D TLITKCAQHA SKLLRKPDQC RAVYLASHLW WATPIAARGE TEDTELYRDG KRVLECLQRA LRVADSCMET ATSIELFVE ILDRYVYYFD QRNESVTTKY LNGLIELIHS NLAGNQQDSA SVEASRKHFI QTLEMIQSKE FEGIVVAPK UniProtKB: ![]() |
-Macromolecule #2: Vacuolar protein sorting-associated protein 29
Macromolecule | Name: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 22.330602 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: SMAFLILVIG NLHIPDRALD IPPKFKKLLS PGKISQTLCL GNLTDRATYD YLRSISPDLK IVRGRMDVEA TSLPLMQVVT HGSLRIGFL EGFTLVSEEP DVLLAEANKL DVDVLCWAGG SHRFECFEYM DKFFVNPGSA TGAFTTDWLA EGEEVVPSFC L MDVQGISL ...String: SMAFLILVIG NLHIPDRALD IPPKFKKLLS PGKISQTLCL GNLTDRATYD YLRSISPDLK IVRGRMDVEA TSLPLMQVVT HGSLRIGFL EGFTLVSEEP DVLLAEANKL DVDVLCWAGG SHRFECFEYM DKFFVNPGSA TGAFTTDWLA EGEEVVPSFC L MDVQGISL TLYVYQLRKD ENGTENVAVE KVTYTKPVEP TGAS UniProtKB: ![]() |
-Experimental details
-Structure determination
Method | ![]() |
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![]() | subtomogram averaging |
Aggregation state | 3D array |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.17 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |