+Open data
-Basic information
Entry | Database: PDB / ID: 7qcd | ||||||
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Title | CryoEM structure of the Smc5/6-holocomplex (composite structure) | ||||||
Components |
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Keywords | RECOMBINATION / Structural Maintenance of Chromosomes / SMC / holo-complex / stalled replication fork | ||||||
Function / homology | Function and homology information Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / Platelet degranulation / protein serine/threonine kinase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / Platelet degranulation / protein serine/threonine kinase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / postreplication repair / SUMO transferase activity / recombinational repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / nuclear envelope / site of double-strand break / single-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / DNA repair / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / zinc ion binding / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | ||||||
Authors | Hallett, S.T. / Oliver, A.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Nucleic Acids Res / Year: 2022 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qcd.cif.gz | 574.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qcd.ent.gz | 436.7 KB | Display | PDB format |
PDBx/mmJSON format | 7qcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qcd_validation.pdf.gz | 787.6 KB | Display | wwPDB validaton report |
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Full document | 7qcd_full_validation.pdf.gz | 930.4 KB | Display | |
Data in XML | 7qcd_validation.xml.gz | 96.3 KB | Display | |
Data in CIF | 7qcd_validation.cif.gz | 144.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/7qcd ftp://data.pdbj.org/pub/pdb/validation_reports/qc/7qcd | HTTPS FTP |
-Related structure data
Related structure data | 13895MC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Structural maintenance of chromosomes protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 126236.180 Da / Num. of mol.: 1 / Mutation: E1015Q Source method: isolated from a genetically manipulated source Details: Saccharomyces cerevisiase Smc5 fused to C-terminal FLAG-tag. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SMC5, YOL034W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q08204 |
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#2: Protein | Mass: 128198.742 Da / Num. of mol.: 1 / Mutation: E1048Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SMC6, RHC18, YLR383W, L3502.2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12749 |
-Protein , 2 types, 2 molecules CD
#3: Protein | Mass: 31817.775 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Saccharomyces cerevisiae Nse2 fused to N-terminal HA-tag. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MMS21, NSE2, YEL019C / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P38632, Transferases; Acyltransferases; Aminoacyltransferases |
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#4: Protein | Mass: 40943.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Saccharomyces cerevisiae Nse1 fused to N-terminal TEV-cleavable His6-tag. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NSE1, YLR007W / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q07913, RING-type E3 ubiquitin transferase |
-Non-structural maintenance of chromosome element ... , 2 types, 2 molecules EF
#5: Protein | Mass: 34005.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Saccharomyces cerevisiae Nse3, untagged. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NSE3, YDR288W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q05541 |
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#6: Protein | Mass: 81441.133 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Saccharomyces cerevisiae Nse4 fused to a C-terminal HALO-myc tag. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NSE4, QRI2, YDL105W, D2354 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43124 |
-Non-polymers , 1 types, 3 molecules
#7: Chemical |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Smc5/6 holo-complex / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Details: Glow-discharged for a period of 60 seconds at 15mA, PELCO easiGlow, Leica Microsystems, Germany. Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K Details: Held in chamber for a period of 10 seconds, before blotting for 2.5 to 4.5 seconds (auto-sensor) then plunged into liquid ethane before being stored under liquid nitrogen. |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 1.3 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 4 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 8 Å / Resolution method: OTHER / Num. of particles: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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