+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33927 | |||||||||
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Title | Cryo-EM structure of Nse1/3/4 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CELL CYCLE | |||||||||
Function / homology | Function and homology information Smc5-Smc6 complex / SUMOylation of DNA damage response and repair proteins / Platelet degranulation / chromatin looping / postreplication repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity ...Smc5-Smc6 complex / SUMOylation of DNA damage response and repair proteins / Platelet degranulation / chromatin looping / postreplication repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / chromosome, telomeric region / DNA repair / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.176 Å | |||||||||
Authors | Qian L / Jun Z / Zhenguo C / Lanfeng W | |||||||||
Funding support | 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2024 Title: Cryo-EM structures of Smc5/6 in multiple states reveal its assembly and functional mechanisms. Authors: Qian Li / Jun Zhang / Cory Haluska / Xiang Zhang / Lei Wang / Guangfeng Liu / Zhaoning Wang / Duo Jin / Tong Cheng / Hongxia Wang / Yuan Tian / Xiangxi Wang / Lei Sun / Xiaolan Zhao / ...Authors: Qian Li / Jun Zhang / Cory Haluska / Xiang Zhang / Lei Wang / Guangfeng Liu / Zhaoning Wang / Duo Jin / Tong Cheng / Hongxia Wang / Yuan Tian / Xiangxi Wang / Lei Sun / Xiaolan Zhao / Zhenguo Chen / Lanfeng Wang / Abstract: Smc5/6 is a member of the eukaryotic structural maintenance of chromosomes (SMC) family of complexes with important roles in genome maintenance and viral restriction. However, limited structural ...Smc5/6 is a member of the eukaryotic structural maintenance of chromosomes (SMC) family of complexes with important roles in genome maintenance and viral restriction. However, limited structural understanding of Smc5/6 hinders the elucidation of its diverse functions. Here, we report cryo-EM structures of the budding yeast Smc5/6 complex in eight-subunit, six-subunit and five-subunit states. Structural maps throughout the entire length of these complexes reveal modularity and key elements in complex assembly. We show that the non-SMC element (Nse)2 subunit supports the overall shape of the complex and uses a wedge motif to aid the stability and function of the complex. The Nse6 subunit features a flexible hook region for attachment to the Smc5 and Smc6 arm regions, contributing to the DNA repair roles of the complex. Our results also suggest a structural basis for the opposite effects of the Nse1-3-4 and Nse5-6 subcomplexes in regulating Smc5/6 ATPase activity. Collectively, our integrated structural and functional data provide a framework for understanding Smc5/6 assembly and function. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33927.map.gz | 9.8 MB | EMDB map data format | |
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Header (meta data) | emd-33927-v30.xml emd-33927.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_33927.png | 79.3 KB | ||
Filedesc metadata | emd-33927.cif.gz | 5.9 KB | ||
Others | emd_33927_half_map_1.map.gz emd_33927_half_map_2.map.gz | 7.9 MB 7.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33927 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33927 | HTTPS FTP |
-Related structure data
Related structure data | 7ymdMC 7ylmC 7yqhC 8hqsC 8i13C 8i21C 8i4uC 8i4vC 8i4wC 8i4xC 8wjlC 8wjnC 8wjoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33927.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.044 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_33927_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_33927_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of Nse1/3/4
Entire | Name: Cryo-EM structure of Nse1/3/4 |
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Components |
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-Supramolecule #1: Cryo-EM structure of Nse1/3/4
Supramolecule | Name: Cryo-EM structure of Nse1/3/4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c |
-Macromolecule #1: Non-structural maintenance of chromosome element 4
Macromolecule | Name: Non-structural maintenance of chromosome element 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 46.195945 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSSTVISRKR RNSTVTEPDS SGETRKQKKS RSDEKSSSSK DGDPQLEFKV LQGYRDLESE MHKGRAQVTR TGDIGVAMDN LNAVDSLFN KVIGIKNNGL FAHDARAMVS ISELAQISVR NLKFDDSRSM VNLENIVNSL KRYMLKEHFK LNNIAENRND L TLAADEQS ...String: MSSTVISRKR RNSTVTEPDS SGETRKQKKS RSDEKSSSSK DGDPQLEFKV LQGYRDLESE MHKGRAQVTR TGDIGVAMDN LNAVDSLFN KVIGIKNNGL FAHDARAMVS ISELAQISVR NLKFDDSRSM VNLENIVNSL KRYMLKEHFK LNNIAENRND L TLAADEQS AADQQEESDG DIDRTPDDNH TDKATSSFKA TSMRHSYLQQ FSHYNEFSQF NWFRIGALYN TISKNAPITD HL MGPLSIE KKPRVLTQRR RNNDQVGEKI TAEKITQHSL NSTQQETTPE QVKKCFKKLS KKLGPEGSIN LFKFIIDPNS FSR SIENLF YTSFLIKEGK LLMEHDEEGL PTIKIKQSIS HTDSRSKEIE RQRRRAAHQN HIIFQMDMPT WRKLIKKYNI TSPF LD UniProtKB: Non-structural maintenance of chromosome element 4 |
-Macromolecule #2: Non-structural maintenance of chromosomes element 1
Macromolecule | Name: Non-structural maintenance of chromosomes element 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 38.373387 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEVHEEQVSA PVTGDATAKY LLQYILSARG ICHENALILA LMRLETDAST LNTEWSIQQW VDKLNDYINA INVKLNLLGY KIIRINHGI GRNAVTLKAK QNFESFEDNT AIRAHNNDYA VLQSIVLPES NRFFVYVNLA STEETKLATR FNQNEIEFMK W AIEQFMIS ...String: MEVHEEQVSA PVTGDATAKY LLQYILSARG ICHENALILA LMRLETDAST LNTEWSIQQW VDKLNDYINA INVKLNLLGY KIIRINHGI GRNAVTLKAK QNFESFEDNT AIRAHNNDYA VLQSIVLPES NRFFVYVNLA STEETKLATR FNQNEIEFMK W AIEQFMIS GETIVEGPAL ETSIIVKEVN RILVAATGDS NLAKWRKFST FTVGSTNLFQ FQELTATDIE DLLLRLCELK WF YRTQEGK FGIDLRCIAE LEEYLTSMYN LNTCQNCHKL AIQGVRCGNE SCREENEETG ENSLSQIWHV DCFKHYITHV SKN CDRCGS SLITEGVYVI UniProtKB: Non-structural maintenance of chromosomes element 1 |
-Macromolecule #3: Non-structural maintenance of chromosome element 3
Macromolecule | Name: Non-structural maintenance of chromosome element 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 34.005531 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSSIDNDSDV DLTEDLAVAK IVKENPVARK MVRYILSRGE SQNSIITRNK LQSVIHEAAR EENIAKPSFS KMFMDINAIL YNVYGFELQ GLPSKNNMNA GGNGSNSNTN KSMPEPLGHR AQKFILLNNV PHSKNFDDFK ILQSAHTYEE LIVTGEYIGD D IASGTSNT ...String: MSSIDNDSDV DLTEDLAVAK IVKENPVARK MVRYILSRGE SQNSIITRNK LQSVIHEAAR EENIAKPSFS KMFMDINAIL YNVYGFELQ GLPSKNNMNA GGNGSNSNTN KSMPEPLGHR AQKFILLNNV PHSKNFDDFK ILQSAHTYEE LIVTGEYIGD D IASGTSNT LESKLSTDRD LVYKGVLSVI LCIVFFSKNN ILHQELIKFL ETFGIPSDGS KIAILNITIE DLIKSLEKRE YI VRLEEKS DTDGEVISYR IGRRTQAELG LESLEKLVQE IMGLEKEQTK SLHDDIIKSI GDSYSI UniProtKB: Non-structural maintenance of chromosome element 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.176 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 610732 |
Initial angle assignment | Type: PROJECTION MATCHING |