8HQS: 8-subunit Smc5/6 head region
Cryo-EM structure of 8-subunit Smc5/6 head region. Determined by electron microscopy at 3.2 Å resolution. Released 19 Jun 2024.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organism
- Saccharomyces cerevisiae S288C
- Chains
- 7
- Atoms
- 19,224
- Mol. weight
- 490.93 kDa
- Released
- 19 Jun 2024
Explore 8HQS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8HQS contains 124 α-helices and 66 β-strands across 7 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 A: 14 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 29-31 | 3 | |
| α-helix | 38 | 1 | |
| β-strand | 42-50 | 9 | 1 |
| β-strand | 53-59 | 7 | 1 |
| β-strand | 65-68 | 4 | 2 |
| α-helix | 75-85 | 11 | |
| α-helix | 90-92 | 3 | |
| α-helix | 99-102 | 4 | |
| β-strand | 109-117 | 9 | 1 |
| β-strand | 134-142 | 9 | 1 |
| β-strand | 149-152 | 4 | 1 |
| β-strand | 156-158 | 3 | 1 |
| α-helix | 159-168 | 10 | |
| β-strand | 179-180 | 2 | 3 |
| α-helix | 182-189 | 8 | |
| α-helix | 193-203 | 11 | |
| α-helix | 207-229 | 23 | |
| α-helix | 913-944 | 32 | |
| β-strand | 953-956 | 4 | 4 |
| α-helix | 961-963 | 3 | |
| β-strand | 965-968 | 4 | 4 |
| α-helix | 988-1001 | 14 | |
| β-strand | 1012-1013 | 2 | 3 |
| α-helix | 1024-1037 | 14 | |
| β-strand | 1045-1046 | 2 | 2 |
| β-strand | 1062-1065 | 4 | 2 |
| α-helix | 1073-1074 | 2 | |
| β-strand | 1083 | 1 | 1 |
Chain B: 19 helices, 18 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 13-35 | 23 | |
| α-helix | 77-78 | 2 | |
| β-strand | 82-88 | 7 | 5 |
| β-strand | 90 | 1 | 6 |
| β-strand | 96-98 | 3 | 5 |
| β-strand | 104-107 | 4 | 7 |
| α-helix | 109-110 | 2 | |
| α-helix | 117-126 | 10 | |
| α-helix | 130-133 | 4 | |
| α-helix | 139-142 | 4 | |
| β-strand | 143 | 1 | 6 |
| α-helix | 144 | 1 | |
| β-strand | 149-157 | 9 | 5 |
| α-helix | 166-169 | 4 | |
| β-strand | 172-180 | 9 | 5 |
| α-helix | 184-185 | 2 | |
| β-strand | 186-188 | 3 | 5 |
| β-strand | 190 | 1 | 8 |
| β-strand | 191 | 1 | 5 |
| β-strand | 196 | 1 | 8 |
| α-helix | 202-211 | 10 | |
| β-strand | 221-222 | 2 | 7 |
| α-helix | 224-231 | 8 | |
| α-helix | 236-246 | 11 | |
| α-helix | 250-279 | 30 | |
| α-helix | 940-983 | 44 | |
| α-helix | 984-986 | 3 | |
| β-strand | 989-995 | 7 | 9 |
| β-strand | 1000-1006 | 7 | 9 |
| β-strand | 1014-1015 | 2 | 9 |
| α-helix | 1021-1036 | 16 | |
| β-strand | 1043-1046 | 4 | 7 |
| α-helix | 1050-1052 | 3 | |
| α-helix | 1056-1070 | 15 | |
| β-strand | 1076-1080 | 5 | 7 |
| α-helix | 1085-1087 | 3 | |
| β-strand | 1096-1099 | 4 | 7 |
Chain D: 19 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 163-172 | 10 | |
| α-helix | 182-189 | 8 | |
| β-strand | 198-199 | 2 | 10 |
| α-helix | 209-220 | 12 | |
| α-helix | 227-229 | 3 | |
| α-helix | 236-242 | 7 | |
| α-helix | 246-253 | 8 | |
| α-helix | 257-261 | 5 | |
| β-strand | 274-275 | 2 | 10 |
| β-strand | 281 | 1 | 11 |
| α-helix | 284-292 | 9 | |
| α-helix | 301-315 | 15 | |
| α-helix | 318-322 | 5 | |
| α-helix | 329-337 | 9 | |
| α-helix | 340-350 | 11 | |
| α-helix | 356-365 | 10 | |
| α-helix | 367-369 | 3 | |
| α-helix | 370-377 | 8 | |
| α-helix | 388-402 | 15 | |
| α-helix | 405-409 | 5 | |
| α-helix | 428-440 | 13 | |
| α-helix | 448-462 | 15 | |
Chain E: 35 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 12 | 1 | 12 |
| β-strand | 22 | 1 | 12 |
| α-helix | 26-40 | 15 | |
| α-helix | 44-53 | 10 | |
| α-helix | 63-65 | 3 | |
| α-helix | 66-75 | 10 | |
| α-helix | 80-90 | 11 | |
| α-helix | 100-116 | 17 | |
| α-helix | 125-141 | 17 | |
| α-helix | 143-147 | 5 | |
| α-helix | 191-194 | 4 | |
| β-strand | 197 | 1 | 13 |
| β-strand | 202 | 1 | 13 |
| α-helix | 203 | 1 | |
| α-helix | 204-208 | 5 | |
| α-helix | 214-224 | 11 | |
| α-helix | 230-235 | 6 | |
| α-helix | 236-240 | 5 | |
| α-helix | 241-257 | 17 | |
| α-helix | 258-262 | 5 | |
| α-helix | 271-277 | 7 | |
| α-helix | 280-286 | 7 | |
| α-helix | 293-301 | 9 | |
| α-helix | 308-309 | 2 | |
| α-helix | 310-312 | 3 | |
| α-helix | 313-315 | 3 | |
| β-strand | 336 | 1 | 11 |
| α-helix | 340-363 | 24 | |
| α-helix | 366 | 1 | |
| α-helix | 378-390 | 13 | |
| α-helix | 395-402 | 8 | |
| α-helix | 414-429 | 16 | |
| α-helix | 434-436 | 3 | |
| α-helix | 438-441 | 4 | |
| α-helix | 445-457 | 13 | |
| α-helix | 463-464 | 2 | |
| α-helix | 472-497 | 26 | |
| α-helix | 506-528 | 23 | |
| α-helix | 534-536 | 3 | |
| α-helix | 539-545 | 7 | |
Chain F: 13 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-27 | 14 | |
| β-strand | 32 | 1 | 14 |
| α-helix | 34-45 | 12 | |
| α-helix | 57-78 | 22 | |
| β-strand | 81-83 | 3 | 15 |
| α-helix | 85 | 1 | |
| β-strand | 86 | 1 | 16 |
| α-helix | 87 | 1 | |
| α-helix | 91-96 | 6 | |
| β-strand | 97 | 1 | 17 |
| β-strand | 100 | 1 | 17 |
| β-strand | 131 | 1 | 16 |
| β-strand | 133 | 1 | 14 |
| β-strand | 134-136 | 3 | 15 |
| α-helix | 152-167 | 16 | |
| α-helix | 183-194 | 12 | |
| β-strand | 206-207 | 2 | 18 |
| α-helix | 215-218 | 4 | |
| α-helix | 224-236 | 13 | |
| β-strand | 240-242 | 3 | 19 |
| β-strand | 248-250 | 3 | 19 |
| α-helix | 252-257 | 6 | |
| α-helix | 261-264 | 4 | |
| β-strand | 282 | 1 | 18 |
| β-strand | 305 | 1 | 18 |
| α-helix | 307-314 | 8 | |
| β-strand | 321 | 1 | 20 |
| β-strand | 326 | 1 | 20 |
| β-strand | 334-335 | 2 | 18 |
Chain G: 17 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-24 | 17 | |
| α-helix | 26-41 | 16 | |
| α-helix | 45 | 1 | |
| β-strand | 46-47 | 2 | 21 |
| α-helix | 48-62 | 15 | |
| α-helix | 65-68 | 4 | |
| α-helix | 69-79 | 11 | |
| α-helix | 80-84 | 5 | |
| β-strand | 86-90 | 5 | 21 |
| α-helix | 94-98 | 5 | |
| β-strand | 122-127 | 6 | 21 |
| α-helix | 135-150 | 16 | |
| α-helix | 178-194 | 17 | |
| β-strand | 199-200 | 2 | 22 |
| α-helix | 201-211 | 11 | |
| α-helix | 218-220 | 3 | |
| α-helix | 227-236 | 10 | |
| β-strand | 240-243 | 4 | 22 |
| β-strand | 255-258 | 4 | 22 |
| α-helix | 260-265 | 6 | |
| α-helix | 268-276 | 9 | |
| α-helix | 283-285 | 3 | |
| α-helix | 290-297 | 8 | |
Chain H: 7 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 222-226 | 5 | |
| α-helix | 242-244 | 3 | |
| β-strand | 305-306 | 2 | 23 |
| α-helix | 309-312 | 4 | |
| α-helix | 320-332 | 13 | |
| β-strand | 340-341 | 2 | 24 |
| β-strand | 347-348 | 2 | 24 |
| β-strand | 349-350 | 2 | 23 |
| α-helix | 360-372 | 13 | |
| α-helix | 374-375 | 2 | |
| α-helix | 384-394 | 11 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Structural maintenance of chromosomes protein 5 | A | protein | 1093 | Saccharomyces cerevisiae S288C | Q08204 (AlphaFold model) |
| Structural maintenance of chromosomes protein 6 | B | protein | 1114 | Saccharomyces cerevisiae S288C | Q12749 (AlphaFold model) |
| DNA repair protein KRE29 | D | protein | 464 | Saccharomyces cerevisiae S288C | P40026 (AlphaFold model) |
| Non-structural maintenance of chromosome element 5 | E | protein | 556 | Saccharomyces cerevisiae S288C | Q03718 (AlphaFold model) |
| Non-structural maintenance of chromosomes element 1 | F | protein | 336 | Saccharomyces cerevisiae S288C | Q07913 |
| Non-structural maintenance of chromosome element 3 | G | protein | 303 | Saccharomyces cerevisiae S288C | Q05541 |
| Non-structural maintenance of chromosome element 4 | H | protein | 402 | Saccharomyces cerevisiae S288C | P43124 |
Sequence of entity 1 (A), FASTA
>8HQS_1 Structural maintenance of chromosomes protein 5 (chains A)
MTSLIDLGRYVERTHHGEDTEPRSKRVKIAKPDLSSFQPGSIIKIRLQDFVTYTLTEFNL
SPSLNMIIGPNGSGKSTFVCAVCLGLAGKPEYIGRSKKVEDFIKNGQDVSKIEITLKNSP
NVTDIEYIDARDETIKITRIITRSKRRSDYLINDYQVSESVVKTLVAQLNIQLDNLCQFL
SQERVEEFARLKSVKLLVETIRSIDASLLDVLDELRELQGNEQSLQKDLDFKKAKIVHLR
QESDKLRKSVESLRDFQNKKGEIELHSQLLPYVKVKDHKEKLNIYKEEYERAKANLRAIL
KDKKPFANTKKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNE
YYRGRTKKLQATIISTKEDFLRSQEILAQTHLPEKSVFEDIDIKRKEIINKEGEIRDLIS
EIDAKANAINHEMRSIQRQAESKTKSLTTTDKIGILNQDQDLKEVRDAVLMVREHPEMKD
KILEPPIMTVSAINAQFAAYLAQCVDYNTSKALTVVDSDSYKLFANPILDKFKVNLRELS
SADTTPPVPAETVRDLGFEGYLSDFITGDKRVMKMLCQTSKIHTIPVSRRELTPAQIKKL
ITPRPNGKILFKRIIHGNRLVDIKQSAYGSKQVFPTDVSIKQTNFYQGSIMSNEQKIRIE
NEIINLKNEYNDRKSTLDALSNQKSGYRHELSELASKNDDINREAHQLNEIRKKYTMRKS
TIETLREKLDQLKREARKDVSQKIKDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQKELI
STQILQFEAQNMDVSMNDVIGFFNEREADLKSQYEDKKKFVKEMRDTPEFQSWMREIRSY
DQDTKEKLNKVAEKYEEEGNFNLSFVQDVLDKLESEIAMVNHDESAVTILDQVTAELREL
EHTVPQQSKDLETIKAKLKEDHAVLEPKLDDIVSKISARFARLFNNVGSAGAVRLEKPKD
YAEWKIEIMVKFRDNAPLKKLDSHTQSGGERAVSTVLYMIALQEFTSAPFRVVDEINQGM
DSRNERIVHKAMVENACAENTSQYFLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPK
MIHFGETSNYSFD
Sequence of entity 2 (B), FASTA
>8HQS_2 Structural maintenance of chromosomes protein 6 (chains B)
MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFR
SSSDVATADQDNFLEESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILT
AITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEIIVERIIK
RDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKY
SHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDL
NERKMLLQAKSLWIDVAHNTDACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTT
IEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQAEAQSNIDQGRKKVDALNKT
IAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSLQDVKNEERDIQHERES
ELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLV
TIRKGFEKWTRSIQRAISSSLNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDY
SKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIEDKNEARNFLQRNPVNVNMAL
SLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYE
EKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQA
IASYEAAKEELGLKIEQIAQEAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKY
KDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNACAFCSKERIENVDLPDTQEEI
KRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKAR
DQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLS
GGEKSFSQMALLLATWKPMRSRIIALDEFDVFMDQVNRKIGTTLIVKKLKDIARTQTIII
TPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYN
Sequence of entity 3 (D), FASTA
>8HQS_3 DNA repair protein KRE29 (chains D)
MGSVNSSPNEEFETVPDSQISGFDSPLIPTSVGSYFRDDDDDEKVHPNFISDPENDSLNS
DEEFSSLENSDLNLSGAKAESGDDFDPILKRTIISKRKAPSNNEDEEIVKTPRKLVNYVP
LKIFNLGDSFDDTITTTVAKLQDLKKEILDSPRSNKSIVITSNTVAKSELQKSIKFSGSI
PEIYLDVVTKETISDKYKDWHFISKNCHYEQLMDLEMKDTAYSFLFGSSRSQGKVPEFVH
LKCPSITNLLVLFGVNQEKCNSLKINYEKKENSRYDNLCTIFPVNKMLKFLMYFYSDDDN
DDVREFFLKAFICLILDRKVFNAMESDHRLCFKVLELFNEAHFINSYFEIVDKNDFFLHY
RLLQIFPHLQSALLRRRFSEKQGRTETIQQNIIKEFNEFFDCKNYKNLLYFILTMYGSKF
IPFGPKCQVTEYFKDCILDISNETTNDVEISILKGILNLFSKIR
Sequence of entity 4 (E), FASTA
>8HQS_4 Non-structural maintenance of chromosome element 5 (chains E)
MDGALINSVLYVSPRNGAHYFVELTEKHLLAFEMLNSMCLLENYDHVLLFLECQFGKSHN
LAVIPFDIILVLFTLSTLSEYYKEPILRANDPYNTSRETLSRRALKLLQKYLAILKEFDS
EQYNLYDLELLRCQFFLAIDTLTPKKQKWGFDRFRRTKSESGVTYRQNASVDPELDQAKT
FKNPYRSYISCLEQRNTILGNRLLNLKLNEPGEFINMILWTLSNSLQESTPLFLSSHEIW
MPLLEILIDLFSCRQDYFIQHEVAQNVSKSLFVQRLSESPLAVFFESLNTRNFANRFSEY
VFLNCDYKLPSDNYATPVHPVYNGENTIVDTYIPTIKCSPLYKSQKSLALRRKLIGSCFK
LLLRVPDGHRLITPRIVADDVIQGISRTLASFNDILQFKKFFMTENLSQESYFIPLLAEG
TLSEILKDTQECVVILTLVENLSDGVSFCNEVIGLVKSKCFAFTEQCSQASYEEAVLNIE
KCDVCLLVLLRYLLHLIGTEAILDAKEQLEMLHAIEKNDSGRRQWAKALNLGNDPPLLYP
IVSQMFGVHDKSVIIE
Sequence of entity 5 (F), FASTA
>8HQS_5 Non-structural maintenance of chromosomes element 1 (chains F)
MEVHEEQVSAPVTGDATAKYLLQYILSARGICHENALILALMRLETDASTLNTEWSIQQW
VDKLNDYINAINVKLNLLGYKIIRINHGIGRNAVTLKAKQNFESFEDNTAIRAHNNDYAV
LQSIVLPESNRFFVYVNLASTEETKLATRFNQNEIEFMKWAIEQFMISGETIVEGPALET
SIIVKEVNRILVAATGDSNLAKWRKFSTFTVGSTNLFQFQELTATDIEDLLLRLCELKWF
YRTQEGKFGIDLRCIAELEEYLTSMYNLNTCQNCHKLAIQGVRCGNESCREENEETGENS
LSQIWHVDCFKHYITHVSKNCDRCGSSLITEGVYVI
Sequence of entity 6 (G), FASTA
>8HQS_6 Non-structural maintenance of chromosome element 3 (chains G)
MSSIDNDSDVDLTEDLAVAKIVKENPVARKMVRYILSRGESQNSIITRNKLQSVIHEAAR
EENIAKPSFSKMFMDINAILYNVYGFELQGLPSKNNMNAGGNGSNSNTNKSMPEPLGHRA
QKFILLNNVPHSKNFDDFKILQSAHTYEELIVTGEYIGDDIASGTSNTLESKLSTDRDLV
YKGVLSVILCIVFFSKNNILHQELIKFLETFGIPSDGSKIAILNITIEDLIKSLEKREYI
VRLEEKSDTDGEVISYRIGRRTQAELGLESLEKLVQEIMGLEKEQTKSLHDDIIKSIGDS
YSI
Sequence of entity 7 (H), FASTA
>8HQS_7 Non-structural maintenance of chromosome element 4 (chains H)
MSSTVISRKRRNSTVTEPDSSGETRKQKKSRSDEKSSSSKDGDPQLEFKVLQGYRDLESE
MHKGRAQVTRTGDIGVAMDNLNAVDSLFNKVIGIKNNGLFAHDARAMVSISELAQISVRN
LKFDDSRSMVNLENIVNSLKRYMLKEHFKLNNIAENRNDLTLAADEQSAADQQEESDGDI
DRTPDDNHTDKATSSFKATSMRHSYLQQFSHYNEFSQFNWFRIGALYNTISKNAPITDHL
MGPLSIEKKPRVLTQRRRNNDQVGEKITAEKITQHSLNSTQQETTPEQVKKCFKKLSKKL
GPEGSINLFKFIIDPNSFSRSIENLFYTSFLIKEGKLLMEHDEEGLPTIKIKQSISHTDS
RSKEIERQRRRAAHQNHIIFQMDMPTWRKLIKKYNITSPFLD
Primary citation
Cryo-EM structures of Smc5/6 in multiple states reveal its assembly and functional mechanisms. Li, Q., Zhang, J., Haluska, C. et al. Nat Struct Mol Biol (2024) 31:1532-1542. DOI 10.1038/s41594-024-01319-1 · PubMed
Other PDB entries of the same protein (UniProt Q08204 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3HTK 2.31 Å, Crystal structure of Mms21 and Smc5 complex
- 7P47 3.31 Å, Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic
- 7TVE 3.8 Å, ATP and DNA bound SMC5/6 core complex
- 8T8F 4.8 Å, Smc5/6 8mer
- 8WJN 5.58 Å, Cryo-EM structure of 6-subunit Smc5/6 head region
- 7YQH 5.6 Å, Cryo-EM structure of 8-subunit Smc5/6
- 8I4V 5.97 Å, Cryo-EM structure of 5-subunit Smc5/6 arm region
- 8I4W 6.01 Å, Cryo-EM structure of 5-subunit Smc5/6 head region
- 8I21 6.02 Å, Cryo-EM structure of 6-subunit Smc5/6 arm region
- 8WJO 6.04 Å, Cryo-EM structure of 8-subunit Smc5/6 arm region
- 8WJL 6.15 Å, Cryo-EM structure of 6-subunit Smc5/6 hinge region
- 7YLM 6.17 Å, Cryo-EM structure of 8-subunit Smc5/6 hinge region
Browse structure collections
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