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- PDB-7sde: Cryo-EM structure of Nse5/6 heterodimer -

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Basic information

Entry
Database: PDB / ID: 7sde
TitleCryo-EM structure of Nse5/6 heterodimer
Components
  • Non-structural maintenance of chromosome element 5
  • Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera
KeywordsSTRUCTURAL 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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / 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 / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / ATPase inhibitor activity / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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
DNA repair protein Nse5/Nse6 / DNA repair proteins Nse5 and Nse6 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
DNA repair protein KRE29 / Non-structural maintenance of chromosome element 5 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYu, Y. / Patel, D.J. / Zhao, X.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM131058 United States
CitationJournal: To Be Published
Title: The cryo-EM structure of Nse5/6 complex with the C terminal part of Nse5
Authors: Yu, Y. / Patel, D.J.
History
DepositionSep 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Non-structural maintenance of chromosome element 5
B: Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera


Theoretical massNumber of molelcules
Total (without water)131,6262
Polymers131,6262
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Non-structural maintenance of chromosome element 5 / Non-SMC element 5


Mass: 63980.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NSE5, YML023C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03718
#2: Protein Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera / 6XHis-SUMO-Nse6


Mass: 67645.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SMT3, YDR510W, D9719.15, KRE29, YER038C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12306, UniProt: P40026

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: heterodimer of Nse5 and Nse6 / Type: COMPLEX
Details: Full length Nse5 without tag Full length Nse6 with a N terminal His-SUMO tag
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.131 MDa / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188986 / Num. of class averages: 1 / Symmetry type: POINT

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