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- PDB-7lto: Nse5-6 complex -

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Basic information

Entry
Database: PDB / ID: 7lto
TitleNse5-6 complex
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 / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication 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 / SUMOylation of DNA damage response and repair proteins / SUMOylation of DNA replication proteins / septin ring / SUMOylation of SUMOylation proteins / chromatin looping / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / 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 / PML body / 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 family / 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. / 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
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM131058 United States
CitationJournal: 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
DepositionFeb 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_db_reference
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)132,9222
Polymers132,9222
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3590 Å2
ΔGint-25 kcal/mol
Surface area27410 Å2

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Components

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


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
#2: Protein Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera / Killer toxin-resistance protein 29


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

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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: Nse5-Nse6 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.133 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 0.3 mg/ml / Embedding 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

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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 FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 47262 X
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1_3660: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 188986 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034864
ELECTRON MICROSCOPYf_angle_d0.5226576
ELECTRON MICROSCOPYf_dihedral_angle_d19.355640
ELECTRON MICROSCOPYf_chiral_restr0.038760
ELECTRON MICROSCOPYf_plane_restr0.003822

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