CryoEM structure of the Smc5/6-holocomplex (composite structure)

2024-07-17 REL PDBe PDBe PDBe 2021-11-23 2022-09-21 2022-09-21 2024-07-17 Medical Research Council (MRC, United Kingdom) MR/PO18955/1 United Kingdom CryoEM structure of the Smc5/6-holocomplex (composite structure) Hallett ST Oliver AW Structural Maintenance of Chromosomes, SMC, holo-complex, recombination, stalled replication fork Hallett ST Campbell Harry I Schellenberger P Zhou L Cronin NB Baxter J Etheridge TJ Murray JM Oliver AW Cryo-EM structure of the Smc5/6 holo-complex. Nucleic Acids Res. UK 50 9505 9520 2022 35993814 doi:10.1093/nar/gkac692 1362-4962 0389 NARHAD EMD-13893 other EM volume

Map for the head-end of the Smc5/6 holo-complex

EMD-13894 other EM volume

Map for the hinge and arm region of the Smc5/6 holo-complex

7qcd FULLOVERLAP Smc5/6 holo-complex Smc5/6 holo-complex 0 1 2 3 4 5 6 Saccharomyces cerevisiae Structural maintenance of chromosomes protein 5 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.12623617999999998

Saccharomyces cerevisiase Smc5 fused to C-terminal FLAG-tag.

1 Spodoptera frugiperda LEVO MTSLIDLGRYVERTHHGEDTEPRSKRVKIAKPDLSSFQPGSIIKIRLQDFVTYTLTEFNLSPSLNMIIGPNGSGKSTFVC AVCLGLAGKPEYIGRSKKVEDFIKNGQDVSKIEITLKNSPNVTDIEYIDARDETIKITRIITRSKRRSDYLINDYQVSES VVKTLVAQLNIQLDNLCQFLSQERVEEFARLKSVKLLVETIRSIDASLLDVLDELRELQGNEQSLQKDLDFKKAKIVHLR QESDKLRKSVESLRDFQNKKGEIELHSQLLPYVKVKDHKEKLNIYKEEYERAKANLRAILKDKKPFANTKKTLENQVEEL TEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYYRGRTKKLQATIISTKEDFLRSQEILAQTHLPEKSVFED IDIKRKEIINKEGEIRDLISEIDAKANAINHEMRSIQRQAESKTKSLTTTDKIGILNQDQDLKEVRDAVLMVREHPEMKD KILEPPIMTVSAINAQFAAYLAQCVDYNTSKALTVVDSDSYKLFANPILDKFKVNLRELSSADTTPPVPAETVRDLGFEG YLSDFITGDKRVMKMLCQTSKIHTIPVSRRELTPAQIKKLITPRPNGKILFKRIIHGNRLVDIKQSAYGSKQVFPTDVSI KQTNFYQGSIMSNEQKIRIENEIINLKNEYNDRKSTLDALSNQKSGYRHELSELASKNDDINREAHQLNEIRKKYTMRKS TIETLREKLDQLKREARKDVSQKIKDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQKELISTQILQFEAQNMDVSMNDVI GFFNEREADLKSQYEDKKKFVKEMRDTPEFQSWMREIRSYDQDTKEKLNKVAEKYEEEGNFNLSFVQDVLDKLESEIAMV NHDESAVTILDQVTAELRELEHTVPQQSKDLETIKAKLKEDHAVLEPKLDDIVSKISARFARLFNNVGSAGAVRLEKPKD YAEWKIEIMVKFRDNAPLKKLDSHTQSGGERAVSTVLYMIALQEFTSAPFRVVDQINQGMDSRNERIVHKAMVENACAEN TSQYFLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPKMIHFGETSNYSFD Q08204 Structural maintenance of chromosomes protein 6 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.128198742 1 Spodoptera frugiperda LEVO MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFRSSSDVATADQDNFLEESPSG YIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILTAITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSK YGAYQQGIFGNEIIVERIIKRDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKY SHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDLNERKMLLQAKSLWIDVAHNT DACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTTIEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQ AEAQSNIDQGRKKVDALNKTIAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSLQDVKNEERDIQHERES ELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLVTIRKGFEKWTRSIQRAISSS LNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDYSKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIE DKNEARNFLQRNPVNVNMALSLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYE EKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQAIASYEAAKEELGLKIEQIAQ EAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKYKDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNAC AFCSKERIENVDLPDTQEEIKRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKAR DQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLSGGEKSFSQMALLLATWKPMR SRIIALDQFDVFMDQVNRKIGTTLIVKKLKDIARTQTIIITPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYN Q12749 E3 SUMO-protein ligase MMS21 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.031817775

Saccharomyces cerevisiae Nse2 fused to N-terminal HA-tag.

1 Spodoptera frugiperda LEVO MGSYPYDVPDYAGSGALNDNPIPKSVPLHPKSGKYFHNLHARDLSNIYQQCYKQIDETINQLVDSTSPSTIGIEEQVADI TSTYKLLSTYESESNSFDEHIKDLKKNFKQSSDACPQIDLSTWDKYRTGELTAPKLSELYLNMPTPEPATMVNNTDTLKI LKVLPYIWNDPTCVIPDLQNPADEDDLQIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAAC SQVVSMRDFVRDPIMELRCKIAKMKESQEQDKRSSQAIDVL P38632 2.3.2.- Non-structural maintenance of chromosomes element 1 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.040943112999999996

Saccharomyces cerevisiae Nse1 fused to N-terminal TEV-cleavable His6-tag.

1 Spodoptera frugiperda LEVO MGSSHHHHHHSSGRENLYFQGHMEVHEEQVSAPVTGDATAKYLLQYILSARGICHENALILALMRLETDASTLNTEWSIQ QWVDKLNDYINAINVKLNLLGYKIIRINHGIGRNAVTLKAKQNFESFEDNTAIRAHNNDYAVLQSIVLPESNRFFVYVNL ASTEETKLATRFNQNEIEFMKWAIEQFMISGETIVEGPALETSIIVKEVNRILVAATGDSNLAKWRKFSTFTVGSTNLFQ FQELTATDIEDLLLRLCELKWFYRTQEGKFGIDLRCIAELEEYLTSMYNLNTCQNCHKLAIQGVRCGNESCREENEETGE NSLSQIWHVDCFKHYITHVSKNCDRCGSSLITEGVYVI Q07913 2.3.2.27 Non-structural maintenance of chromosome element 3 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.034005531

Saccharomyces cerevisiae Nse3, untagged.

1 Spodoptera frugiperda LEVO MSSIDNDSDVDLTEDLAVAKIVKENPVARKMVRYILSRGESQNSIITRNKLQSVIHEAAREENIAKPSFSKMFMDINAIL YNVYGFELQGLPSKNNMNAGGNGSNSNTNKSMPEPLGHRAQKFILLNNVPHSKNFDDFKILQSAHTYEELIVTGEYIGDD IASGTSNTLESKLSTDRDLVYKGVLSVILCIVFFSKNNILHQELIKFLETFGIPSDGSKIAILNITIEDLIKSLEKREYI VRLEEKSDTDGEVISYRIGRRTQAELGLESLEKLVQEIMGLEKEQTKSLHDDIIKSIGDSYSI Q05541 Non-structural maintenance of chromosome element 4 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) ATCC 204508 / S288c 0.081441133

Saccharomyces cerevisiae Nse4 fused to a C-terminal HALO-myc tag.

1 Spodoptera frugiperda LEVO MSSTVISRKRRNSTVTEPDSSGETRKQKKSRSDEKSSSSKDGDPQLEFKVLQGYRDLESEMHKGRAQVTRTGDIGVAMDN LNAVDSLFNKVIGIKNNGLFAHDARAMVSISELAQISVRNLKFDDSRSMVNLENIVNSLKRYMLKEHFKLNNIAENRNDL TLAADEQSAADQQEESDGDIDRTPDDNHTDKATSSFKATSMRHSYLQQFSHYNEFSQFNWFRIGALYNTISKNAPITDHL MGPLSIEKKPRVLTQRRRNNDQVGEKITAEKITQHSLNSTQQETTPEQVKKCFKKLSKKLGPEGSINLFKFIIDPNSFSR SIENLFYTSFLIKEGKLLMEHDEEGLPTIKIKQSISHTDSRSKEIERQRRRAAHQNHIIFQMDMPTWRKLIKKYNITSPF LDGSSGMAEIGTGFPFDPHYVEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDK PDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRPIPTWDEWPEFARETFQAFRT TDVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYREPFLNPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPV PKLLFWGTPGVLIPPAEAARLAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTLEISGGSEQKLISEEDL P43124 ZINC ION 6.5409e-05 3 ZN singleParticle particle 0.1 7.5 20.0 C8H18N2O4S HEPES 50.0 NaCl sodium chloride 0.5 C9H16ClO6P TCEP Quantifoil R0.6/1 COPPER 300 GLOW DISCHARGE 60

Glow-discharged for a period of 60 seconds at 15mA, PELCO easiGlow, Leica Microsystems, Germany.

ETHANE 90 293 LEICA EM GP

Held in chamber for a period of 10 seconds, before blotting for 2.5 to 4.5 seconds (auto-sensor) then plunged into liquid ethane before being stored under liquid nitrogen..

FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 NITROGEN GATAN K3 (6k x 4k) 4 1.3 1 8.0 OTHER cryoSPARC 3.1.0 1 ANGULAR RECONSTITUTION cryoSPARC 3.1.0 MAXIMUM LIKELIHOOD cryoSPARC 3.1.0 emd_13895.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 320 320 320 0 0 0 320 320 320 704.0 704.0 704.0 90.0 90.0 90.0 Z Y X -65.910804999999996 132.47829999999999 -0.022724925 0.9486908 2.2 2.2 2.2 11.0 AUTHOR ::::EMDATABANK.org::::EMD-13895:::: CryoEM structure of the Smc5/6 holocomplex; composite map OTHER REAL