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Title | Cryo-EM structure of 8-subunit Smc5/6 head region | |||||||||
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![]() | CELL CYCLE | |||||||||
Function / homology | ![]() Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMOylation of DNA damage response and repair proteins / Platelet degranulation / ATPase inhibitor activity / chromatin looping / postreplication repair / recombinational repair ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMOylation of DNA damage response and repair proteins / Platelet degranulation / ATPase inhibitor activity / chromatin looping / postreplication repair / recombinational repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / site of double-strand break / single-stranded DNA binding / chromosome, telomeric region / damaged DNA binding / DNA repair / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Qian L / Jun Z / Xiang Z / Tong C / Wang Z / Duo J / Zhenguo C / Wang L | |||||||||
Funding support | 1 items
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 922.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.2 KB 24.2 KB | Display Display | ![]() |
Images | ![]() | 51.8 KB | ||
Filedesc metadata | ![]() | 8.2 KB | ||
Others | ![]() ![]() | 926.4 MB 926.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hqsMC ![]() 7ylmC ![]() 7ymdC ![]() 7yqhC ![]() 8i13C ![]() 8i21C ![]() 8i4uC ![]() 8i4vC ![]() 8i4wC ![]() 8i4xC ![]() 8wjlC ![]() 8wjnC ![]() 8wjoC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34953_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34953_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of 8-subunit Smc5/6 head region
Entire | Name: Cryo-EM structure of 8-subunit Smc5/6 head region |
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Components |
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-Supramolecule #1: Cryo-EM structure of 8-subunit Smc5/6 head region
Supramolecule | Name: Cryo-EM structure of 8-subunit Smc5/6 head region / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #5-#6, #1-#4, #7 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Structural maintenance of chromosomes protein 5
Macromolecule | Name: Structural maintenance of chromosomes protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 126.237164 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Structural maintenance of chromosomes protein 6
Macromolecule | Name: Structural maintenance of chromosomes protein 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 128.199727 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: DNA repair protein KRE29
Macromolecule | Name: DNA repair protein KRE29 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 53.836758 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSVNSSPNE EFETVPDSQI SGFDSPLIPT SVGSYFRDDD DDEKVHPNFI SDPENDSLNS DEEFSSLENS DLNLSGAKAE SGDDFDPIL KRTIISKRKA PSNNEDEEIV KTPRKLVNYV PLKIFNLGDS FDDTITTTVA KLQDLKKEIL DSPRSNKSIV I TSNTVAKS ...String: MGSVNSSPNE EFETVPDSQI SGFDSPLIPT SVGSYFRDDD DDEKVHPNFI SDPENDSLNS DEEFSSLENS DLNLSGAKAE SGDDFDPIL KRTIISKRKA PSNNEDEEIV KTPRKLVNYV PLKIFNLGDS FDDTITTTVA KLQDLKKEIL DSPRSNKSIV I TSNTVAKS ELQKSIKFSG SIPEIYLDVV TKETISDKYK DWHFISKNCH YEQLMDLEMK DTAYSFLFGS SRSQGKVPEF VH LKCPSIT NLLVLFGVNQ EKCNSLKINY EKKENSRYDN LCTIFPVNKM LKFLMYFYSD DDNDDVREFF LKAFICLILD RKV FNAMES DHRLCFKVLE LFNEAHFINS YFEIVDKNDF FLHYRLLQIF PHLQSALLRR RFSEKQGRTE TIQQNIIKEF NEFF DCKNY KNLLYFILTM YGSKFIPFGP KCQVTEYFKD CILDISNETT NDVEISILKG ILNLFSKIR UniProtKB: DNA repair protein KRE29 |
-Macromolecule #4: Non-structural maintenance of chromosome element 5
Macromolecule | Name: Non-structural maintenance of chromosome element 5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 64.079609 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MDGALINSVL YVSPRNGAHY FVELTEKHLL AFEMLNSMCL LENYDHVLLF LECQFGKSHN LAVIPFDIIL VLFTLSTLSE YYKEPILRA NDPYNTSRET LSRRALKLLQ KYLAILKEFD SEQYNLYDLE LLRCQFFLAI DTLTPKKQKW GFDRFRRTKS E SGVTYRQN ...String: MDGALINSVL YVSPRNGAHY FVELTEKHLL AFEMLNSMCL LENYDHVLLF LECQFGKSHN LAVIPFDIIL VLFTLSTLSE YYKEPILRA NDPYNTSRET LSRRALKLLQ KYLAILKEFD SEQYNLYDLE LLRCQFFLAI DTLTPKKQKW GFDRFRRTKS E SGVTYRQN ASVDPELDQA KTFKNPYRSY ISCLEQRNTI LGNRLLNLKL NEPGEFINMI LWTLSNSLQE STPLFLSSHE IW MPLLEIL IDLFSCRQDY FIQHEVAQNV SKSLFVQRLS ESPLAVFFES LNTRNFANRF SEYVFLNCDY KLPSDNYATP VHP VYNGEN TIVDTYIPTI KCSPLYKSQK SLALRRKLIG SCFKLLLRVP DGHRLITPRI VADDVIQGIS RTLASFNDIL QFKK FFMTE NLSQESYFIP LLAEGTLSEI LKDTQECVVI LTLVENLSDG VSFCNEVIGL VKSKCFAFTE QCSQASYEEA VLNIE KCDV CLLVLLRYLL HLIGTEAILD AKEQLEMLHA IEKNDSGRRQ WAKALNLGND PPLLYPIVSQ MFGVHDKSVI IE UniProtKB: Non-structural maintenance of chromosome element 5 |
-Macromolecule #5: Non-structural maintenance of chromosomes element 1
Macromolecule | Name: Non-structural maintenance of chromosomes element 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: RING-type E3 ubiquitin transferase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 38.373387 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #6: Non-structural maintenance of chromosome element 3
Macromolecule | Name: Non-structural maintenance of chromosome element 3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 34.005531 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #7: Non-structural maintenance of chromosome element 4
Macromolecule | Name: Non-structural maintenance of chromosome element 4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 46.195945 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 546112 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |