+Open data
-Basic information
Entry | Database: PDB / ID: 7lto | ||||||
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Title | Nse5-6 complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / SMC5/6 / Nse5-6 / Nse5 / Nse6 / complex / SUMO-binding | ||||||
Function / homology | Function and homology information Smc5-Smc6 complex / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins ...Smc5-Smc6 complex / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / SUMO is proteolytically processed / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / ATPase inhibitor activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / chromatin looping / SUMOylation of chromatin organization proteins / regulation of telomere maintenance / ubiquitin-like protein ligase binding / protein sumoylation / condensed nuclear chromosome / double-strand break repair via homologous recombination / protein tag activity / chromosome, telomeric region / DNA repair / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Yu, Y. / Li, S.B. / Zheng, S. / Tangy, S. / Koyi, C. / Wan, B.B. / Kung, H.H. / Andrej, S. / Alex, K. / Patel, D.J. / Zhao, X.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Integrative analysis reveals unique structural and functional features of the Smc5/6 complex. Authors: You Yu / Shibai Li / Zheng Ser / Tanmoy Sanyal / Koyi Choi / Bingbing Wan / Huihui Kuang / Andrej Sali / Alex Kentsis / Dinshaw J Patel / Xiaolan Zhao / Abstract: Structural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC complexes organize chromatin, while the Smc5/6 complex directly ...Structural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC complexes organize chromatin, while the Smc5/6 complex directly regulates DNA replication and repair. The molecular basis for the distinct functions of Smc5/6 is poorly understood. Here, we report an integrative structural study of the budding yeast Smc5/6 holo-complex using electron microscopy, cross-linking mass spectrometry, and computational modeling. We show that the Smc5/6 complex possesses several unique features, while sharing some architectural characteristics with other SMC complexes. In contrast to arm-folded structures of cohesin and condensin, Smc5 and Smc6 arm regions do not fold back on themselves. Instead, these long filamentous regions interact with subunits uniquely acquired by the Smc5/6 complex, namely the Nse2 SUMO ligase and the Nse5/Nse6 subcomplex, with the latter also serving as a linchpin connecting distal parts of the complex. Our 3.0-Å resolution cryoelectron microscopy structure of the Nse5/Nse6 core further reveals a clasped-hand topology and a dimeric interface important for cell growth. Finally, we provide evidence that Nse5/Nse6 uses its SUMO-binding motifs to contribute to Nse2-mediated sumoylation. Collectively, our integrative study identifies distinct structural features of the Smc5/6 complex and functional cooperation among its coevolved unique subunits. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lto.cif.gz | 130.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lto.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 7lto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lto_validation.pdf.gz | 798.4 KB | Display | wwPDB validaton report |
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Full document | 7lto_full_validation.pdf.gz | 807.9 KB | Display | |
Data in XML | 7lto_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 7lto_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/7lto ftp://data.pdbj.org/pub/pdb/validation_reports/lt/7lto | HTTPS FTP |
-Related structure data
Related structure data | 23517MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 65276.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: NSE5, YML023C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03718 |
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#2: Protein | Mass: 67645.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SMT3, YDR510W, D9719.15, KRE29, YER038C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12306, UniProt: P40026 |
-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: Nse5-Nse6 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.133 MDa / Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE |
-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 / Nominal magnification: 22500 X / Calibrated magnification: 47262 X |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188986 / Symmetry type: POINT | ||||||||||||||||||||||||
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