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- EMDB-33927: Cryo-EM structure of Nse1/3/4 -

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Basic information

Entry
Database: EMDB / ID: EMD-33927
TitleCryo-EM structure of Nse1/3/4
Map data
Sample
  • Complex: Cryo-EM structure of Nse1/3/4
    • Protein or peptide: Non-structural maintenance of chromosome element 4
    • Protein or peptide: Non-structural maintenance of chromosomes element 1
    • Protein or peptide: Non-structural maintenance of chromosome element 3
KeywordsCELL CYCLE
Function / homology
Function and homology information


Smc5-Smc6 complex / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / chromatin looping / DNA damage tolerance / regulation of telomere maintenance / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / chromosome, telomeric region ...Smc5-Smc6 complex / Platelet degranulation / SUMOylation of DNA damage response and repair proteins / chromatin looping / DNA damage tolerance / regulation of telomere maintenance / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / chromosome, telomeric region / DNA repair / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / MAGE homology domain ...Non-structural maintenance of chromosomes element 1 / Zinc finger, RING-like / Nse1 non-SMC component of SMC5-6 complex / RING-like domain / Non-structural maintenance of chromosome element 4, C-terminal / Nse4/EID family / Nse4/EID protein, Nse3/MAGE-binding domain / Nse4 C-terminal / Binding domain of Nse4/EID3 to Nse3-MAGE / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Non-structural maintenance of chromosome element 4 / Non-structural maintenance of chromosome element 3 / Non-structural maintenance of chromosomes element 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.176 Å
AuthorsQian L / Jun Z / Zhenguo C / Lanfeng W
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: 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
DepositionJul 28, 2022-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33927.png

Downloads & links

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Map

FileDownload / File: emd_33927.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 140 pix.
= 146.16 Å		1.04 Å/pix.
x 140 pix.
= 146.16 Å		1.04 Å/pix.
x 140 pix.
= 146.16 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.044 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.12097661 - 0.17885552
Average (Standard dev.)-0.00012040859 (±0.006752209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 146.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33927_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33927_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of Nse1/3/4

EntireName: Cryo-EM structure of Nse1/3/4
Components
  • Complex: Cryo-EM structure of Nse1/3/4
    • Protein or peptide: Non-structural maintenance of chromosome element 4
    • Protein or peptide: Non-structural maintenance of chromosomes element 1
    • Protein or peptide: Non-structural maintenance of chromosome element 3

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Supramolecule #1: Cryo-EM structure of Nse1/3/4

SupramoleculeName: Cryo-EM structure of Nse1/3/4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast) / Strain: S288c

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Macromolecule #1: Non-structural maintenance of chromosome element 4

MacromoleculeName: Non-structural maintenance of chromosome element 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 46.195945 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Non-structural maintenance of chromosomes element 1

MacromoleculeName: 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
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 38.373387 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #3: Non-structural maintenance of chromosome element 3

MacromoleculeName: Non-structural maintenance of chromosome element 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c
Molecular weightTheoretical: 34.005531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.176 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 610732
Initial angle assignmentType: PROJECTION MATCHING

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