+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35185 | |||||||||
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Title | Cryo-EM structure of 5-subunit Smc5/6 arm region | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CELL CYCLE | |||||||||
Function / homology | Function and homology information Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / ATPase inhibitor activity / protein serine/threonine kinase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases ...Smc5-Smc6 complex / resolution of DNA recombination intermediates / DNA double-strand break attachment to nuclear envelope / chromosome separation / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / ATPase inhibitor activity / protein serine/threonine kinase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity / recombinational repair / regulation of telomere maintenance / protein sumoylation / double-strand break repair via homologous recombination / nuclear envelope / site of double-strand break / single-stranded DNA binding / damaged DNA binding / chromosome, telomeric region / DNA repair / ATP hydrolysis activity / mitochondrion / zinc ion binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.97 Å | |||||||||
Authors | Qian L / Jun Z / Xiang Z / Cheng T / Zhaoning W / Zhenguo C / Wang L | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35185.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-35185-v30.xml emd-35185.xml | 19.1 KB 19.1 KB | Display Display | EMDB header |
Images | emd_35185.png | 40.2 KB | ||
Filedesc metadata | emd-35185.cif.gz | 7 KB | ||
Others | emd_35185_half_map_1.map.gz emd_35185_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35185 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35185 | HTTPS FTP |
-Validation report
Summary document | emd_35185_validation.pdf.gz | 706.1 KB | Display | EMDB validaton report |
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Full document | emd_35185_full_validation.pdf.gz | 705.7 KB | Display | |
Data in XML | emd_35185_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_35185_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35185 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35185 | HTTPS FTP |
-Related structure data
Related structure data | 8i4vMC 7ylmC 7ymdC 7yqhC 8hqsC 8i13C 8i21C 8i4uC 8i4wC 8i4xC 8wjlC 8wjnC 8wjoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35185.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 2.128 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35185_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35185_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of 5-subunit Smc5/6 arm region
Entire | Name: Cryo-EM structure of 5-subunit Smc5/6 arm region |
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Components |
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-Supramolecule #1: Cryo-EM structure of 5-subunit Smc5/6 arm region
Supramolecule | Name: Cryo-EM structure of 5-subunit Smc5/6 arm region / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-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: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 123.390031 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: KRVKIAKPDL SSFQPGSIIK IRLQDFVTYT LTEFNLSPSL NMIIGPNGSG KSTFVCAVCL GLAGKPEYIG RSKKVEDFIK NGQDVSKIE ITLKNSPNVT DIEYIDARDE TIKITRIITR SKRRSDYLIN DYQVSESVVK TLVAQLNIQL DNLCQFLSQE R VEEFARLK ...String: KRVKIAKPDL SSFQPGSIIK IRLQDFVTYT LTEFNLSPSL NMIIGPNGSG KSTFVCAVCL GLAGKPEYIG RSKKVEDFIK NGQDVSKIE ITLKNSPNVT DIEYIDARDE TIKITRIITR SKRRSDYLIN DYQVSESVVK TLVAQLNIQL DNLCQFLSQE R VEEFARLK SVKLLVETIR SIDASLLDVL DELRELQGNE QSLQKDLDFK KAKIVHLRQE SDKLRKSVES LRDFQNKKGE IE LHSQLLP YVKVKDHKEK LNIYKEEYER AKANLRAILK DKKPFANTKK TLENQVEELT EKCSLKTDEF LKAKEKINEI FEK LNTIRD EVIKKKNQNE YYRGRTKKLQ ATIISTKEDF LRSQEILAQT HLPEKSVFED IDIKRKEIIN KEGEIRDLIS EIDA KANAI NHEMRSIQRQ AESKTKSLTT TDKIGILNQD QDLKEVRDAV LMVREHPEMK DKILEPPIMT VSAINAQFAA YLAQC VDYN TSKALTVVDS DSYKLFANPI LDKFKVNLRE LSSADTTPPV PAETVRDLGF EGYLSDFITG DKRVMKMLCQ TSKIHT IPV SRRELTPAQI KKLITPRPNG KILFKRIIHG NRLVDIKQSA YGSKQVFPTD VSIKQTNFYQ GSIMSNEQKI RIENEII NL KNEYNDRKST LDALSNQKSG YRHELSELAS KNDDINREAH QLNEIRKKYT MRKSTIETLR EKLDQLKREA RKDVSQKI K DIDDQIQQLL LKQRHLLSKM ASSMKSLKNC QKELISTQIL QFEAQNMDVS MNDVIGFFNE READLKSQYE DKKKFVKEA RDTPEFQSWM REIRSYDQDT KEKLNKVAEK YEEEGNFNLS FVQDVLDKLE SEIAMVNHDE SAVTILDQVT AELRELEHTV PQQSKDLET IKAKLKEDHA VLEPKLDDIV SKISARFARL FNNVGSAGAV RLEKPKDYAE WKIEIMVKFR DNAPLKKLDS H TQSGGERA VSTVLYMIAL QEFTSAPFRV VDEINQGMDS RNERIVHKAM VENACAENTS QYFLITPKLL TGLHYHEKMR IH CVMAGSW IPNPSEDPKM IHFGETSNYS FD 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: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 128.199727 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
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: E3 SUMO-protein ligase MMS21
Macromolecule | Name: E3 SUMO-protein ligase MMS21 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO EC number: Transferases; Acyltransferases; Aminoacyltransferases |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 28.600305 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: NDNPIPKSVP LHPKSGKYFH NLHARDLSNI YQQCYKQIDE TINQLVDSTS PSTIGIEEQV ADITSTYKLL STYESESNSF DEHIKDLKK NFKQSSDACP QIDLSTWDKY RTGELTAPKL SELYLNMPTP EPATMVNNTD TLKILKVLPY IWNDPTCVIP D LQNPADED ...String: NDNPIPKSVP LHPKSGKYFH NLHARDLSNI YQQCYKQIDE TINQLVDSTS PSTIGIEEQV ADITSTYKLL STYESESNSF DEHIKDLKK NFKQSSDACP QIDLSTWDKY RTGELTAPKL SELYLNMPTP EPATMVNNTD TLKILKVLPY IWNDPTCVIP D LQNPADED DLQIEGGKIE LTCPITCKPY EAPLISRKCN HVFDRDGIQN YLQGYTTRDC PQAACSQVVS MRDFVRDPIM EL RCKIAKM KESQ UniProtKB: E3 SUMO-protein ligase MMS21 |
-Macromolecule #4: DNA repair protein KRE29
Macromolecule | Name: DNA repair protein KRE29 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: S288c |
Molecular weight | Theoretical: 7.337511 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: PILKRTIISK RKAPSNNEDE EIVKTPRKLV NYVPLKIFNL GDSFDDTITT TVAKLQDLKK EILD UniProtKB: DNA repair protein KRE29 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227122 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |