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- EMDB-13893: Cryo-EM structure of the Smc5/6 holo-complex; map for head-end of... -
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Open data
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Basic information
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Title | Cryo-EM structure of the Smc5/6 holo-complex; map for head-end of complex. | |||||||||
![]() | CryoEM structure of the Smc5/6 holo-complex; map for the head-end of the complex. | |||||||||
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![]() | Structural Maintenance of Chromosomes / SMC / holo-complex / recombination / stalled replication fork | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
![]() | OLIVER AW / Hallett ST | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the Smc5/6 holo-complex. Authors: Stephen T Hallett / Isabella Campbell Harry / Pascale Schellenberger / Lihong Zhou / Nora B Cronin / Jonathan Baxter / Thomas J Etheridge / Johanne M Murray / Antony W Oliver / ![]() Abstract: The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also ...The Smc5/6 complex plays an essential role in the resolution of recombination intermediates formed during mitosis or meiosis, or as a result of the cellular response to replication stress. It also functions as a restriction factor preventing viral replication. Here, we report the cryogenic EM (cryo-EM) structure of the six-subunit budding yeast Smc5/6 holo-complex, reconstituted from recombinant proteins expressed in insect cells - providing both an architectural overview of the entire complex and an understanding of how the Nse1/3/4 subcomplex binds to the hetero-dimeric SMC protein core. In addition, we demonstrate that a region within the head domain of Smc5, equivalent to the 'W-loop' of Smc4 or 'F-loop' of Smc1, mediates an important interaction with Nse1. Notably, mutations that alter the surface-charge profile of the region of Nse1 which accepts the Smc5-loop, lead to a slow-growth phenotype and a global reduction in the chromatin-associated fraction of the Smc5/6 complex, as judged by single molecule localisation microscopy experiments in live yeast. Moreover, when taken together, our data indicates functional equivalence between the structurally unrelated KITE and HAWK accessory subunits associated with SMC complexes. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 5.5 KB | Display | ![]() |
Images | ![]() | 43.9 KB | ||
Masks | ![]() | 15.6 MB | ![]() | |
Filedesc metadata | ![]() | 4.4 KB | ||
Others | ![]() ![]() | 14.5 MB 14.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | CryoEM structure of the Smc5/6 holo-complex; map for the head-end of the complex. | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Half-map B for the head-end of the Smc5/6 holo-complex.
File | emd_13893_half_map_1.map | ||||||||||||
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Annotation | Half-map B for the head-end of the Smc5/6 holo-complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map A for the head-end of the Smc5/6 holo-complex.
File | emd_13893_half_map_2.map | ||||||||||||
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Annotation | Half-map A for the head-end of the Smc5/6 holo-complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Saccharomyces cerevisiae Smc5/6 holo-complex
Entire | Name: Saccharomyces cerevisiae Smc5/6 holo-complex |
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Components |
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-Supramolecule #1: Saccharomyces cerevisiae Smc5/6 holo-complex
Supramolecule | Name: Saccharomyces cerevisiae Smc5/6 holo-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Map focussed at the head-end of the holo0complex |
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Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP Details: The grid was held in the chamber for a period of 10 seconds, before blotting for 2.5 to 4.5 seconds using the auto-sensor. Grids were then plunged into liquid ethane before being stored ...Details: The grid was held in the chamber for a period of 10 seconds, before blotting for 2.5 to 4.5 seconds using the auto-sensor. Grids were then plunged into liquid ethane before being stored under liquid nitrogen until data collection.. | ||||||||||||
Details | Fraction(s) eluting from a Superose 6 size exclusion chromatography column (Cytiva Life Sciences). Cross-linked with BS3 before grid preparation. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Average exposure time: 4.0 sec. / Average electron dose: 1.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |