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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cryo-EM structure of 5-subunit Smc5/6 arm 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 / SUMO ligase activity / SUMOylation of DNA damage response and repair proteins / protein serine/threonine kinase inhibitor activity / chromatin looping / Transferases; Acyltransferases; Aminoacyltransferases / SUMO transferase activity ...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 / 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 / chromosome, telomeric region / damaged DNA binding / DNA repair / ATP hydrolysis activity / mitochondrion / zinc ion binding / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.97 Å | |||||||||
![]() | Qian L / Jun Z / Xiang Z / Cheng T / Zhaoning W / 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 L / Jun Z / Xiang Z / Wang Z / Tong C / Duo J / Zhenguo C / Wang L | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
Images | ![]() | 40.2 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() | 115.9 MB 115.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 706.3 KB | Display | ![]() |
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Full document | ![]() | 705.9 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 16 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8i4vMC ![]() 7ylmC ![]() 7yqhC ![]() 8hqsC ![]() 8i13C ![]() 8i21C ![]() 8i4uC ![]() 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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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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 |
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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: ![]() ![]() |
-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: 123.390031 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() ![]() |
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: 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: ![]() ![]() |
Molecular weight | Theoretical: 28.600305 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() ![]() |
Molecular weight | Theoretical: 7.337511 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | 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: 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 |