Title | Retromer-Vps5: low-resolution overview map centred on the Vps26 dimer. |
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Authors | Kovtun O, Leneva N, Ariotti N, Rohan TS, Owen DJ, Briggs JAG, Collins BM |
Method | Subtomogram Averaging(Reported Resolution 11.4 Å)PDB:6h7w |
Primary Citation | Structure 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 |
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Funding Source | Wellcome Trust, Medical Research Council (United Kingdom), Australian Research Council, National Health and Medical Research Council (Australia) |
Status | Deposited | Released | Last Update |
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REL | 2018-07-31 | 2018-09-26 | 2024-05-15 |
Name: Retromer-Vps5 complex assembled on the membrane.SpecimenType: threeDArray MW: 0.751 MDa pH: 7.5
Component Types | complex |
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Component Names | Retromer-Vps5 complex assembled on the membrane. |
Molecular Types | protein |
Molecule Names |
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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 Preparation | vitrification |
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Vitrification | LEICA EM GP |
Microscope | FEI TITAN KRIOS (300 kV) |
Specimen Holder | FEI TITAN KRIOS AUTOGRID HOLDER |
Detector | GATAN K2 QUANTUM (4k x 4k) |
Electron Dose | 3.17 (e/sq. Å) |
Imposed Symmetry | C2 |
Fitting Protocol | FLEXIBLE FIT |
Details: Low-resolution overview map of retromer-Vps5 centered on the Vps26 dimer.
Map File Size | 12 Mbytes |
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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 Statistics | Min -0.535Max 0.765Avg 0.003Std 0.058 |
Recommended Contour Level | 0.15 (2.5 σ) |
Header Metadata | emd-0154.xml emd-0154.cif.gz |
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Primary Map | emd_0154.map.gz (12 Mbytes) |
Images | emd_0154.png |
Fitted PDB | 6h7w |
Current: files.wwpdb.org (USA)
wwPDB Map Validation Report | emd_0154_full_validation.pdf.gz |
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wwPDB Model Validation Report | 6h7w_full_validation.pdf.gz |