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- EMDB-35116: Cryo-EM structure of 6-subunit Smc5/6 -

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Basic information

Entry
Database: EMDB / ID: EMD-35116
TitleCryo-EM structure of 6-subunit Smc5/6
Map data
Sample
  • Complex: Cryo-EM structure of 6-subunit Smc5/6
    • Protein or peptide: SMC6 isoform 1
    • Protein or peptide: Structural maintenance of chromosomes protein 5
    • Protein or peptide: MMS21 isoform 1
    • Protein or peptide: Non-structural maintenance of chromosomes element 1 homolog
    • Protein or peptide: NSE3 isoform 1
    • Protein or peptide: Non-structural maintenance of chromosomes element 4
KeywordsCELL CYCLE
Function / homology
Function and homology information


Smc5-Smc6 complex / SUMO ligase activity / protein sumoylation / chromosome segregation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / single-stranded DNA binding / site of double-strand break / DNA recombination ...Smc5-Smc6 complex / SUMO ligase activity / protein sumoylation / chromosome segregation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / single-stranded DNA binding / site of double-strand break / DNA recombination / damaged DNA binding / DNA repair / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / zinc ion binding / ATP binding / nucleus / metal ion binding
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 / E3 SUMO-protein ligase Nse2 (Mms21) ...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 / E3 SUMO-protein ligase Nse2 (Mms21) / Zinc-finger of the MIZ type in Nse subunit / Structural maintenance of chromosomes protein 5 / Zinc finger, MIZ-type / Zinc finger SP-RING-type profile. / 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 / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Zinc finger, RING/FYVE/PHD-type / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Non-structural maintenance of chromosomes element 4 / Structural maintenance of chromosomes protein 5 / SMC6 isoform 1 / Non-structural maintenance of chromosomes element 1 homolog / MMS21 isoform 1 / NSE3 isoform 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsQian L / Jun Z / Xiang Z / Tong C / Zhaoning W / Duo J / 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
DepositionJan 12, 2023-
Header (metadata) releaseJun 26, 2024-
Map releaseJun 26, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35116.png

Downloads & links

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Map

FileDownload / File: emd_35116.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 320 pix.
= 680.96 Å		2.13 Å/pix.
x 320 pix.
= 680.96 Å		2.13 Å/pix.
x 320 pix.
= 680.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.128 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum0.0 - 7.3944235
Average (Standard dev.)0.001541365 (±0.03764799)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 680.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of 6-subunit Smc5/6

EntireName: Cryo-EM structure of 6-subunit Smc5/6
Components
  • Complex: Cryo-EM structure of 6-subunit Smc5/6
    • Protein or peptide: SMC6 isoform 1
    • Protein or peptide: Structural maintenance of chromosomes protein 5
    • Protein or peptide: MMS21 isoform 1
    • Protein or peptide: Non-structural maintenance of chromosomes element 1 homolog
    • Protein or peptide: NSE3 isoform 1
    • Protein or peptide: Non-structural maintenance of chromosomes element 4

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Supramolecule #1: Cryo-EM structure of 6-subunit Smc5/6

SupramoleculeName: Cryo-EM structure of 6-subunit Smc5/6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: SMC6 isoform 1

MacromoleculeName: SMC6 isoform 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 128.199727 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MISTTISGKR PIEQVDDELL SLTAQQENEE QQQQRKRRRH QFAPMTQFNS NTLDEDSGFR SSSDVATADQ DNFLEESPSG YIKKVILRN FMCHEHFELE LGSRLNFIVG NNGSGKSAIL TAITIGLGAK ASETNRGSSL KDLIREGCYS AKIILHLDNS K YGAYQQGI ...String:
MISTTISGKR PIEQVDDELL SLTAQQENEE QQQQRKRRRH QFAPMTQFNS NTLDEDSGFR SSSDVATADQ DNFLEESPSG YIKKVILRN FMCHEHFELE LGSRLNFIVG NNGSGKSAIL TAITIGLGAK ASETNRGSSL KDLIREGCYS AKIILHLDNS K YGAYQQGI FGNEIIVERI IKRDGPASFS LRSENGKEIS NKKKDIQTVV DYFSVPVSNP MCFLSQDAAR SFLTASTSQD KY SHFMKGT LLQEITENLL YASAIHDSAQ ENMALHLENL KSLKAEYEDA KKLLRELNQT SDLNERKMLL QAKSLWIDVA HNT DACKNL ENEISGIQQK VDEVTEKIRN RQEKIERYTS DGTTIEAQID AKVIYVNEKD SEHQNARELL RDVKSRFEKE KSNQ AEAQS NIDQGRKKVD ALNKTIAHLE EELTKEMGGD KDQMRQELEQ LEKANEKLRE VNNSLVVSLQ DVKNEERDIQ HERES ELRT ISRSIQNKKV ELQNIAKGND TFLMNFDRNM DRLLRTIEQR KNEFETPAIG PLGSLVTIRK GFEKWTRSIQ RAISSS LNA FVVSNPKDNR LFRDIMRSCG IRSNIPIVTY CLSQFDYSKG RAHGNYPTIV DALEFSKPEI ECLFVDLSRI ERIVLIE DK NEARNFLQRN PVNVNMALSL RDRRSGFQLS GGYRLDTVTY QDKIRLKVNS SSDNGTQYLK DLIEQETKEL QNIRDRYE E KLSEVRSRLK EIDGRLKSTK NEMRKTNFRM TELKMNVGKV VDTGILNSKI NERKNQEQAI ASYEAAKEEL GLKIEQIAQ EAQPIKEQYD STKLALVEAQ DELQQLKEDI NSRQSKIQKY KDDTIYYEDK KKVYLENIKK IEVNVAALKE GIQRQIQNAC AFCSKERIE NVDLPDTQEE IKRELDKVSR MIQKAEKSLG LSQEEVIALF EKCRNKYKEG QKKYMEIDEA LNRLHNSLKA R DQNYKNAE KGTCFDADMD FRASLKVRKF SGNLSFIKDT KSLEIYILTT NDEKARNVDT LSGGEKSFSQ MALLLATWKP MR SRIIALD EFDVFMDQVN RKIGTTLIVK KLKDIARTQT IIITPQDIGK IADIDSSGVS IHRMRDPERQ NNSNFYN

UniProtKB: SMC6 isoform 1

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Macromolecule #2: Structural maintenance of chromosomes protein 5

MacromoleculeName: Structural maintenance of chromosomes protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 126.237164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MTSLIDLGRY VERTHHGEDT EPRSKRVKIA KPDLSSFQPG SIIKIRLQDF VTYTLTEFNL SPSLNMIIGP NGSGKSTFVC AVCLGLAGK PEYIGRSKKV EDFIKNGQDV SKIEITLKNS PNVTDIEYID ARDETIKITR IITRSKRRSD YLINDYQVSE S VVKTLVAQ ...String:
MTSLIDLGRY VERTHHGEDT EPRSKRVKIA KPDLSSFQPG SIIKIRLQDF VTYTLTEFNL SPSLNMIIGP NGSGKSTFVC AVCLGLAGK PEYIGRSKKV EDFIKNGQDV SKIEITLKNS PNVTDIEYID ARDETIKITR IITRSKRRSD YLINDYQVSE S VVKTLVAQ LNIQLDNLCQ FLSQERVEEF ARLKSVKLLV ETIRSIDASL LDVLDELREL QGNEQSLQKD LDFKKAKIVH LR QESDKLR KSVESLRDFQ NKKGEIELHS QLLPYVKVKD HKEKLNIYKE EYERAKANLR AILKDKKPFA NTKKTLENQV EEL TEKCSL KTDEFLKAKE KINEIFEKLN TIRDEVIKKK NQNEYYRGRT KKLQATIIST KEDFLRSQEI LAQTHLPEKS VFED IDIKR KEIINKEGEI RDLISEIDAK ANAINHEMRS IQRQAESKTK SLTTTDKIGI LNQDQDLKEV RDAVLMVREH PEMKD KILE PPIMTVSAIN AQFAAYLAQC VDYNTSKALT VVDSDSYKLF ANPILDKFKV NLRELSSADT TPPVPAETVR DLGFEG YLS DFITGDKRVM KMLCQTSKIH TIPVSRRELT PAQIKKLITP RPNGKILFKR IIHGNRLVDI KQSAYGSKQV FPTDVSI KQ TNFYQGSIMS NEQKIRIENE IINLKNEYND RKSTLDALSN QKSGYRHELS ELASKNDDIN REAHQLNEIR KKYTMRKS T IETLREKLDQ LKREARKDVS QKIKDIDDQI QQLLLKQRHL LSKMASSMKS LKNCQKELIS TQILQFEAQN MDVSMNDVI GFFNEREADL KSQYEDKKKF VKEMRDTPEF QSWMREIRSY DQDTKEKLNK VAEKYEEEGN FNLSFVQDVL DKLESEIAMV NHDESAVTI LDQVTAELRE LEHTVPQQSK DLETIKAKLK EDHAVLEPKL DDIVSKISAR FARLFNNVGS AGAVRLEKPK D YAEWKIEI MVKFRDNAPL KKLDSHTQSG GERAVSTVLY MIALQEFTSA PFRVVDEINQ GMDSRNERIV HKAMVENACA EN TSQYFLI TPKLLTGLHY HEKMRIHCVM AGSWIPNPSE DPKMIHFGET SNYSFD

UniProtKB: Structural maintenance of chromosomes protein 5

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Macromolecule #3: MMS21 isoform 1

MacromoleculeName: MMS21 isoform 1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.388336 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALNDNPIPK SVPLHPKSGK YFHNLHARDL SNIYQQCYKQ IDETINQLVD STSPSTIGIE EQVADITSTY KLLSTYESES NSFDEHIKD LKKNFKQSSD ACPQIDLSTW DKYRTGELTA PKLSELYLNM PTPEPATMVN NTDTLKILKV LPYIWNDPTC V IPDLQNPA ...String:
MALNDNPIPK SVPLHPKSGK YFHNLHARDL SNIYQQCYKQ IDETINQLVD STSPSTIGIE EQVADITSTY KLLSTYESES NSFDEHIKD LKKNFKQSSD ACPQIDLSTW DKYRTGELTA PKLSELYLNM PTPEPATMVN NTDTLKILKV LPYIWNDPTC V IPDLQNPA DEDDLQIEGG KIELTCPITC KPYEAPLISR KCNHVFDRDG IQNYLQGYTT RDCPQAACSQ VVSMRDFVRD PI MELRCKI AKMKESQEQD KRSSQAIDVL

UniProtKB: MMS21 isoform 1

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Macromolecule #4: Non-structural maintenance of chromosomes element 1 homolog

MacromoleculeName: Non-structural maintenance of chromosomes element 1 homolog
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 38.373387 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 homolog

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Macromolecule #5: NSE3 isoform 1

MacromoleculeName: NSE3 isoform 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 34.005531 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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: NSE3 isoform 1

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Macromolecule #6: Non-structural maintenance of chromosomes element 4

MacromoleculeName: Non-structural maintenance of chromosomes element 4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 46.195945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 chromosomes element 4

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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 K3 BIOQUANTUM (6k 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: 2.2 µm / Nominal defocus min: 1.2 µm
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: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1000000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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