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- EMDB-23517: Nse5-6 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-23517
TitleNse5-6 complex
Map data
Sample
  • Complex: Nse5-Nse6 complex
    • Protein or peptide: Non-structural maintenance of chromosome element 5
    • Protein or peptide: Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera
KeywordsSMC5/6 / Nse5-6 / Nse5 / Nse6 / complex / SUMO-binding / STRUCTURAL PROTEIN
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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYu Y / Li SB
Funding support United States, 1 items
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, 2021-
Header (metadata) releaseMay 19, 2021-
Map releaseMay 19, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-7lto
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sde
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7lto
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23517.png

Downloads & links

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Map

FileDownload / File: emd_23517.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 280 pix.
= 297.92 Å		1.06 Å/pix.
x 280 pix.
= 297.92 Å		1.06 Å/pix.
x 280 pix.
= 297.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.013 / Movie #1: 0.02
Minimum - Maximum-0.111277156 - 0.19337769
Average (Standard dev.)-0.0000025385355 (±0.002780942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 297.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z297.920297.920297.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.1110.193-0.000

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Supplemental data

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Sample components

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Entire : Nse5-Nse6 complex

EntireName: Nse5-Nse6 complex
Components
  • Complex: Nse5-Nse6 complex
    • Protein or peptide: Non-structural maintenance of chromosome element 5
    • Protein or peptide: Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera

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Supramolecule #1: Nse5-Nse6 complex

SupramoleculeName: Nse5-Nse6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 133 KDa

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Macromolecule #1: Non-structural maintenance of chromosome element 5

MacromoleculeName: Non-structural maintenance of chromosome element 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 65.276961 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MADLNWISAG HMDGALINSV LYVSPRNGAH YFVELTEKHL LAFEMLNSMC LLENYDHVLL FLECQFGKSH NLAVIPFDII LVLFTLSTL SEYYKEPILR ANDPYNTSRE TLSRRALKLL QKYLAILKEF DSEQYNLYDL ELLRCQFFLA IDTLTPKKQK W GFDRFRRT ...String:
MADLNWISAG HMDGALINSV LYVSPRNGAH YFVELTEKHL LAFEMLNSMC LLENYDHVLL FLECQFGKSH NLAVIPFDII LVLFTLSTL SEYYKEPILR ANDPYNTSRE TLSRRALKLL QKYLAILKEF DSEQYNLYDL ELLRCQFFLA IDTLTPKKQK W GFDRFRRT KSESGVTYRQ NASVDPELDQ AKTFKNPYRS YISCLEQRNT ILGNRLLNLK LNEPGEFINM ILWTLSNSLQ ES TPLFLSS HEIWMPLLEI LIDLFSCRQD YFIQHEVAQN VSKSLFVQRL SESPLAVFFE SLNTRNFANR FSEYVFLNCD YKL PSDNYA TPVHPVYNGE NTIVDTYIPT IKCSPLYKSQ KSLALRRKLI GSCFKLLLRV PDGHRLITPR IVADDVIQGI SRTL ASFND ILQFKKFFMT ENLSQESYFI PLLAEGTLSE ILKDTQECVV ILTLVENLSD GVSFCNEVIG LVKSKCFAFT EQCSQ ASYE EAVLNIEKCD VCLLVLLRYL LHLIGTEAIL DAKEQLEMLH AIEKNDSGRR QWAKALNLGN DPPLLYPIVS QMFGVH DKS VIIE

UniProtKB: Non-structural maintenance of chromosome element 5

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Macromolecule #2: Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera

MacromoleculeName: Ubiquitin-like protein SMT3,DNA repair protein KRE29 chimera
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 67.64518 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASMSDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLRFL YDGIRIQADQ TPEDLDMEDN DIIEAHREQI GGSMGSVNSS PNEEFETVPD SQISGFDSPL IPTSVGSYFR D DDDDEKVH ...String:
MGSSHHHHHH SSGLVPRGSH MASMSDSEVN QEAKPEVKPE VKPETHINLK VSDGSSEIFF KIKKTTPLRR LMEAFAKRQG KEMDSLRFL YDGIRIQADQ TPEDLDMEDN DIIEAHREQI GGSMGSVNSS PNEEFETVPD SQISGFDSPL IPTSVGSYFR D DDDDEKVH PNFISDPEND SLNSDEEFSS LENSDLNLSG AKAESGDDFD PILKRTIISK RKAPSNNEDE EIVKTPRKLV NY VPLKIFN LGDSFDDTIT TTVAKLQDLK KEILDSPRSN KSIVITSNTV AKSELQKSIK FSGSIPEIYL DVVTKETISD KYK DWHFIS KNCHYEQLMD LEMKDTAYSF LFGSSRSQGK VPEFVHLKCP SITNLLVLFG VNQEKCNSLK INYEKKENSR YDNL CTIFP VNKMLKFLMY FYSDDDNDDV REFFLKAFIC LILDRKVFNA MESDHRLCFK VLELFNEAHF INSYFEIVDK NDFFL HYRL LQIFPHLQSA LLRRRFSEKQ GRTETIQQNI IKEFNEFFDC KNYKNLLYFI LTMYGSKFIP FGPKCQVTEY FKDCIL DIS NETTNDVEIS ILKGILNLFS KIR

UniProtKB: Ubiquitin-like protein SMT3, DNA repair protein KRE29

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47262 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 22500
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188986
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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