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TitleRetromer-Vps5: low-resolution overview map centred on the Vps26 dimer.
AuthorsKovtun O, Leneva N, Ariotti N, Rohan TS, Owen DJ, Briggs JAG, Collins BM
MethodSubtomogram Averaging(Reported Resolution 11.4 Å)PDB:6h7w
EMDB image
Primary CitationStructure of the membrane-assembled retromer coat determined by cryo-electron tomography. Kovtun O, Leneva N, Bykov YS, Ariotti N, Teasdale RD, Schaffer M, Engel BD, Owen DJ, Briggs JAG, Collins BM Nature (2018) PubMed DOI show all entries for this citation
Funding SourceWellcome Trust, Medical Research Council (United Kingdom), Australian Research Council, National Health and Medical Research Council (Australia)
StatusDepositedReleasedLast Update
REL2018-07-312018-09-262024-05-15

Name: Retromer-Vps5 complex assembled on the membrane.SpecimenType: threeDArray MW: 0.751 MDa pH: 7.5

Component Typescomplex
Component Names

Retromer-Vps5 complex assembled on the membrane.

Molecular Typesprotein
Molecule Names
  • Putative vacuolar protein sorting-associated protein
  • Vacuolar protein sorting-associated protein 26-like protein
  • Vacuolar protein sorting-associated protein 29
  • Vacuolar protein sorting-associated protein 35
Sources

Chaetomium thermophilum var.... ncbi:759272

Chaetomium thermophilum (strain... ncbi:759272

Specimen Preparation Details: The solution-assembled complex was incubated with Folch liposomes at room temperature.

Imaging Details: Tomographic tilt series were acquired with the dose-symmetric tilt-scheme (Hagen et al., J Struct Biol. 2017)

Fitting Details: Note that the associated PDB model was not generated by fitting into this map! It was generated by fitting into the associated local high-resolution maps and then combined. Initial global ridgid body fitting was done using Chimera, followed by MDFF within NAMD for flexible fitting. Note that side chain positions are not reliable in model generated by refinement into a map at this resolution.

Specimen Preparationvitrification
VitrificationLEICA EM GP
MicroscopeFEI TITAN KRIOS (300 kV)
Specimen HolderFEI TITAN KRIOS AUTOGRID HOLDER
DetectorGATAN K2 QUANTUM (4k x 4k)
Electron Dose3.17 (e/sq. Å)
Imposed SymmetryC2
Fitting ProtocolFLEXIBLE FIT

Details: Low-resolution overview map of retromer-Vps5 centered on the Vps26 dimer.

Map File Size12 Mbytes
Voxel Dimensions (Å)2.7 x 2.7 x 2.7
Map Dimensions (voxels) 144 x 144 x 144
Map Data Type IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Density StatisticsMin -0.535Max 0.765Avg 0.003Std 0.058
Recommended Contour Level0.15 (2.5 σ)
Mol*3DViewer Map Visual Analysis @ EMDB
Header Metadataemd-0154.xml emd-0154.cif.gz
Primary Mapemd_0154.map.gz (12 Mbytes)
Imagesemd_0154.png
Fitted PDB6h7w


Current: files.wwpdb.org (USA)

wwPDB Map Validation Reportemd_0154_full_validation.pdf.gz
wwPDB Model Validation Report6h7w_full_validation.pdf.gz
View EMDB map entry EMD-0154: EMDB PDBj 3Dbionotes
View associated model PDB 6h7w: RCSB-PDB PDBe PDBj