8T8F: Smc5/6 8mer

Smc5/6 8mer. Determined by electron microscopy at 4.8 Å resolution. Released 15 Nov 2023.

Method
Electron microscopy
Resolution
4.8 Å
Organism
Saccharomyces cerevisiae W303
Chains
5
Atoms
13,050
Mol. weight
418.55 kDa
Released
15 Nov 2023

Explore 8T8F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T8F contains 77 α-helices and 39 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 17 helices, 1 β-strand

ElementResiduesLengthSheet
α-helix206-2072
α-helix209-21911
α-helix246-2538
α-helix271-2733
β-strand28111
α-helix284-2918
α-helix292-2943
α-helix301-31515
α-helix318-3225
α-helix330-3356
α-helix340-3456
α-helix357-3626
α-helix367-3693
α-helix370-3778
α-helix388-40013
α-helix407-4159
α-helix433-4397
α-helix451-46111
Chain C: 27 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix23-253
α-helix26-4015
α-helix44-529
α-helix63-653
α-helix66-7611
α-helix84-907
α-helix100-11516
α-helix125-14016
β-strand19812
β-strand20112
α-helix205-2084
α-helix216-2238
α-helix230-2345
α-helix242-26019
α-helix269-2724
α-helix274-2763
α-helix280-2856
α-helix297-3004
α-helix314-3174
β-strand33611
α-helix340-35617
α-helix359-3646
α-helix389-3913
α-helix395-4028
α-helix414-42916
α-helix439-4413
α-helix445-45713
α-helix472-49726
α-helix506-52823
α-helix539-5468
Chain D: 15 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix37-382
β-strand42-4873
β-strand5014
β-strand55-5733
β-strand65-6845
α-helix78-858
α-helix90-923
α-helix99-1024
β-strand10314
α-helix1041
β-strand110-11783
β-strand134-14183
β-strand150-15233
β-strand156-15723
α-helix159-16810
β-strand179-18026
α-helix184-1885
α-helix193-20412
α-helix206-24540
α-helix884-94562
β-strand950-95677
α-helix961-9633
β-strand965-97177
α-helix988-100215
β-strand1010-101346
α-helix1022-103615
α-helix1041-10422
β-strand1043-104536
β-strand1046-104725
β-strand1062-106545
α-helix1079-10813
Chain E: 12 helices, 16 β-strands
ElementResiduesLengthSheet
β-strand85-8848
β-strand9019
β-strand9319
α-helix116-1249
α-helix131-1333
α-helix140-1423
β-strand14319
β-strand145110
β-strand147110
β-strand149-15578
β-strand174-18078
α-helix1851
β-strand186-19058
β-strand196-19838
α-helix201-2077
α-helix225-2306
α-helix236-24611
α-helix249-28638
α-helix924-96542
α-helix972-9809
β-strand989-992411
β-strand1003-1006411
α-helix1022-103615
β-strand1043-1044212
β-strand1047113
α-helix1055-106915
β-strand1076-1077212
β-strand1080113
Chain G: 6 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix289-2957
α-helix296-3005
β-strand305-306214
α-helix320-33314
β-strand337-339314
β-strand349-351314
α-helix363-37210
α-helix376-3783
α-helix385-3884

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA repair protein KRE29Bprotein464Saccharomyces cerevisiae W303P40026 (AlphaFold model)
Non-structural maintenance of chromosome element 5Cprotein556Saccharomyces cerevisiae W303Q03718 (AlphaFold model)
Structural maintenance of chromosomes protein 5Dprotein1093Saccharomyces cerevisiae W303Q08204 (AlphaFold model)
Structural maintenance of chromosomes protein 6Eprotein1114Saccharomyces cerevisiae W303Q12749 (AlphaFold model)
Non-structural maintenance of chromosome element 4Gprotein402Saccharomyces cerevisiae W303P43124
Sequence of entity 1 (B), FASTA
>8T8F_1 DNA repair protein KRE29 (chains B)
MGSVNSSPNEEFETVPDSQISGFDSPLIPTSVGSYFRDDDDDEKVHPNFISDPENDSLNS
DEEFSSLENSDLNLSGAKAESGDDFDPILKRTIISKRKAPSNNEDEEIVKTPRKLVNYVP
LKIFNLGDSFDDTITTTVAKLQDLKKEILDSPRSNKSIVITSNTVAKSELQKSIKFSGSI
PEIYLDVVTKETISDKYKDWHFISKNCHYEQLMDLEMKDTAYSFLFGSSRSQGKVPEFVH
LKCPSITNLLVLFGVNQEKCNSLKINYEKKENSRYDNLCTIFPVNKMLKFLMYFYSDDDN
DDVREFFLKAFICLILDRKVFNAMESDHRLCFKVLELFNEAHFINSYFEIVDKNDFFLHY
RLLQIFPHLQSALLRRRFSEKQGRTETIQQNIIKEFNEFFDCKNYKNLLYFILTMYGSKF
IPFGPKCQVTEYFKDCILDISNETTNDVEISILKGILNLFSKIR
Sequence of entity 2 (C), FASTA
>8T8F_2 Non-structural maintenance of chromosome element 5 (chains C)
MDGALINSVLYVSPRNGAHYFVELTEKHLLAFEMLNSMCLLENYDHVLLFLECQFGKSHN
LAVIPFDIILVLFTLSTLSEYYKEPILRANDPYNTSRETLSRRALKLLQKYLAILKEFDS
EQYNLYDLELLRCQFFLAIDTLTPKKQKWGFDRFRRTKSESGVTYRQNASVDPELDQAKT
FKNPYRSYISCLEQRNTILGNRLLNLKLNEPGEFINMILWTLSNSLQESTPLFLSSHEIW
MPLLEILIDLFSCRQDYFIQHEVAQNVSKSLFVQRLSESPLAVFFESLNTRNFANRFSEY
VFLNCDYKLPSDNYATPVHPVYNGENTIVDTYIPTIKCSPLYKSQKSLALRRKLIGSCFK
LLLRVPDGHRLITPRIVADDVIQGISRTLASFNDILQFKKFFMTENLSQESYFIPLLAEG
TLSEILKDTQECVVILTLVENLSDGVSFCNEVIGLVKSKCFAFTEQCSQASYEEAVLNIE
KCDVCLLVLLRYLLHLIGTEAILDAKEQLEMLHAIEKNDSGRRQWAKALNLGNDPPLLYP
IVSQMFGVHDKSVIIE
Sequence of entity 3 (D), FASTA
>8T8F_3 Structural maintenance of chromosomes protein 5 (chains D)
MTSLIDLGRYVERTHHGEDTEPRSKRVKIAKPDLSSFQPGSIIKIRLQDFVTYTLTEFNL
SPSLNMIIGPNGSGKSTFVCAVCLGLAGKPEYIGRSKKVEDFIKNGQDVSKIEITLKNSP
NVTDIEYIDARDETIKITRIITRSKRRSDYLINDYQVSESVVKTLVAQLNIQLDNLCQFL
SQERVEEFARLKSVKLLVETIRSIDASLLDVLDELRELQGNEQSLQKDLDFKKAKIVHLR
QESDKLRKSVESLRDFQNKKGEIELHSQLLPYVKVKDHKEKLNIYKEEYERAKANLRAIL
KDKKPFANTKKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNE
YYRGRTKKLQATIISTKEDFLRSQEILAQTHLPEKSVFEDIDIKRKEIINKEGEIRDLIS
EIDAKANAINHEMRSIQRQAESKTKSLTTTDKIGILNQDQDLKEVRDAVLMVREHPEMKD
KILEPPIMTVSAINAQFAAYLAQCVDYNTSKALTVVDSDSYKLFANPILDKFKVNLRELS
SADTTPPVPAETVRDLGFEGYLSDFITGDKRVMKMLCQTSKIHTIPVSRRELTPAQIKKL
ITPRPNGKILFKRIIHGNRLVDIKQSAYGSKQVFPTDVSIKQTNFYQGSIMSNEQKIRIE
NEIINLKNEYNDRKSTLDALSNQKSGYRHELSELASKNDDINREAHQLNEIRKKYTMRKS
TIETLREKLDQLKREARKDVSQKIKDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQKELI
STQILQFEAQNMDVSMNDVIGFFNEREADLKSQYEDKKKFVKEMRDTPEFQSWMREIRSY
DQDTKEKLNKVAEKYEEEGNFNLSFVQDVLDKLESEIAMVNHDESAVTILDQVTAELREL
EHTVPQQSKDLETIKAKLKEDHAVLEPKLDDIVSKISARFARLFNNVGSAGAVRLEKPKD
YAEWKIEIMVKFRDNAPLKKLDSHTQSGGERAVSTVLYMIALQEFTSAPFRVVDQINQGM
DSRNERIVHKAMVENACAENTSQYFLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPK
MIHFGETSNYSFD
Sequence of entity 4 (E), FASTA
>8T8F_4 Structural maintenance of chromosomes protein 6 (chains E)
MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFR
SSSDVATADQDNFLEESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILT
AITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEIIVERIIK
RDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKY
SHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDL
NERKMLLQAKSLWIDVAHNTDACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTT
IEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQAEAQSNIDQGRKKVDALNKT
IAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSLQDVKNEERDIQHERES
ELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLV
TIRKGFEKWTRSIQRAISSSLNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDY
SKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIEDKNEARNFLQRNPVNVNMAL
SLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYE
EKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQA
IASYEAAKEELGLKIEQIAQEAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKY
KDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNACAFCSKERIENVDLPDTQEEI
KRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKAR
DQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLS
GGEKSFSQMALLLATWKPMRSRIIALDQFDVFMDQVNRKIGTTLIVKKLKDIARTQTIII
TPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYN
Sequence of entity 5 (G), FASTA
>8T8F_5 Non-structural maintenance of chromosome element 4 (chains G)
MSSTVISRKRRNSTVTEPDSSGETRKQKKSRSDEKSSSSKDGDPQLEFKVLQGYRDLESE
MHKGRAQVTRTGDIGVAMDNLNAVDSLFNKVIGIKNNGLFAHDARAMVSISELAQISVRN
LKFDDSRSMVNLENIVNSLKRYMLKEHFKLNNIAENRNDLTLAADEQSAADQQEESDGDI
DRTPDDNHTDKATSSFKATSMRHSYLQQFSHYNEFSQFNWFRIGALYNTISKNAPITDHL
MGPLSIEKKPRVLTQRRRNNDQVGEKITAEKITQHSLNSTQQETTPEQVKKCFKKLSKKL
GPEGSINLFKFIIDPNSFSRSIENLFYTSFLIKEGKLLMEHDEEGLPTIKIKQSISHTDS
RSKEIERQRRRAAHQNHIIFQMDMPTWRKLIKKYNITSPFLD

Primary citation

Molecular basis for Nse5-6 mediated regulation of Smc5/6 functions. Li, S., Yu, Y., Zheng, J. et al. Proc Natl Acad Sci U S A (2023) 120:e2310924120-e2310924120. DOI 10.1073/pnas.2310924120 · PubMed

Other PDB entries of the same protein (UniProt P40026 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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