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- EMDB-37584: Cryo-EM structure of 6-subunit Smc5/6 hinge region -

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Basic information

Entry
Database: EMDB / ID: EMD-37584
TitleCryo-EM structure of 6-subunit Smc5/6 hinge region
Map data
Sample
  • Complex: 6-subunit Smc5/6 complex
    • Protein or peptide: Structural maintenance of chromosomes protein 6
    • Protein or peptide: Structural maintenance of chromosomes protein 5
    • Protein or peptide: E3 SUMO-protein ligase MMS21
Keywordscell cycle
Function / homology
Function and homology information


Smc5-Smc6 complex / resolution of DNA recombination intermediates / chromosome separation / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / protein serine/threonine kinase inhibitor activity / SUMO transferase activity ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / chromosome separation / DNA double-strand break attachment to nuclear envelope / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / protein serine/threonine kinase inhibitor activity / SUMO transferase activity / recombinational repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / nuclear envelope / single-stranded DNA binding / site of double-strand break / damaged DNA binding / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / mitochondrion / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
E3 SUMO-protein ligase MMS21, N-terminal domain / 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. / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain ...E3 SUMO-protein ligase MMS21, N-terminal domain / 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. / Rad50/SbcC-type AAA domain / AAA domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
E3 SUMO-protein ligase MMS21 / Structural maintenance of chromosomes protein 5 / Structural maintenance of chromosomes protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.15 Å
AuthorsLi Q / Zhang J / Zhang X / Cheng T / Wang Z / Jin D / Chen Z / Wang L
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
DepositionSep 26, 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_37584.png

Downloads & links

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Map

FileDownload / File: emd_37584.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: 0.3
Minimum - Maximum-4.323285 - 7.263336
Average (Standard dev.)-0.0010641005 (±0.056116384)
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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Half map: #2

Fileemd_37584_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_37584_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 6-subunit Smc5/6 complex

EntireName: 6-subunit Smc5/6 complex
Components
  • Complex: 6-subunit Smc5/6 complex
    • Protein or peptide: Structural maintenance of chromosomes protein 6
    • Protein or peptide: Structural maintenance of chromosomes protein 5
    • Protein or peptide: E3 SUMO-protein ligase MMS21

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Supramolecule #1: 6-subunit Smc5/6 complex

SupramoleculeName: 6-subunit Smc5/6 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

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Macromolecule #1: Structural maintenance of chromosomes protein 6

MacromoleculeName: Structural maintenance of chromosomes protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (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: Structural maintenance of chromosomes protein 6

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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 S288C (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: E3 SUMO-protein ligase MMS21

MacromoleculeName: E3 SUMO-protein ligase MMS21 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Aminoacyltransferases
Source (natural)Organism: Saccharomyces cerevisiae S288C (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: E3 SUMO-protein ligase MMS21

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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 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 179509
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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