7TVE: ATP and DNA bound SMC5/6 core complex
ATP and DNA bound SMC5/6 core complex. Determined by electron microscopy at 3.8 Å resolution. Released 22 Jun 2022.
- Method
- Electron microscopy
- Resolution
- 3.8 Å
- Organisms
- synthetic construct, Saccharomyces cerevisiae W303
- Chains
- 7
- Atoms
- 15,456
- Mol. weight
- 423.06 kDa
- Ligands
- ATP
- Released
- 22 Jun 2022
Explore 7TVE in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7TVE contains 66 α-helices and 56 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 C: 12 helices, 10 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-27 | 14 | |
| β-strand | 32-33 | 2 | 1 |
| α-helix | 34-47 | 14 | |
| α-helix | 57-78 | 22 | |
| β-strand | 80-86 | 7 | 1 |
| α-helix | 91-99 | 9 | |
| β-strand | 131-137 | 7 | 1 |
| α-helix | 143-145 | 3 | |
| α-helix | 152-170 | 19 | |
| β-strand | 173-174 | 2 | 2 |
| α-helix | 176-178 | 3 | |
| α-helix | 182-195 | 14 | |
| β-strand | 205-207 | 3 | 2 |
| α-helix | 213-216 | 4 | |
| α-helix | 224-236 | 13 | |
| β-strand | 242 | 1 | 3 |
| β-strand | 248 | 1 | 3 |
| α-helix | 261-264 | 4 | |
| β-strand | 281-283 | 3 | 2 |
| β-strand | 304-305 | 2 | 2 |
| α-helix | 307-315 | 9 | |
| β-strand | 333-335 | 3 | 2 |
Chain D: 14 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 84-90 | 7 | 4 |
| β-strand | 93-99 | 7 | 4 |
| β-strand | 105-108 | 4 | 5 |
| α-helix | 116-124 | 9 | |
| α-helix | 131-133 | 3 | |
| α-helix | 139-141 | 3 | |
| β-strand | 143 | 1 | 4 |
| β-strand | 145 | 1 | 6 |
| β-strand | 147 | 1 | 6 |
| β-strand | 149-155 | 7 | 4 |
| β-strand | 174-180 | 7 | 4 |
| α-helix | 184-185 | 2 | |
| β-strand | 186-190 | 5 | 4 |
| β-strand | 196 | 1 | 4 |
| α-helix | 201-211 | 11 | |
| β-strand | 221 | 1 | 5 |
| α-helix | 227-232 | 6 | |
| α-helix | 236-246 | 11 | |
| α-helix | 249-294 | 46 | |
| α-helix | 308-310 | 3 | |
| α-helix | 904-915 | 12 | |
| α-helix | 922-983 | 62 | |
| β-strand | 990-993 | 4 | 7 |
| β-strand | 1002-1005 | 4 | 7 |
| α-helix | 1013-1014 | 2 | |
| α-helix | 1022-1032 | 11 | |
| β-strand | 1043-1047 | 5 | 5 |
| α-helix | 1055-1071 | 17 | |
| β-strand | 1076-1080 | 5 | 5 |
| β-strand | 1098-1100 | 3 | 5 |
Chain E: 12 helices, 17 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-38 | 2 | |
| β-strand | 42-48 | 7 | 8 |
| β-strand | 55-57 | 3 | 8 |
| β-strand | 64-68 | 5 | 9 |
| α-helix | 78-85 | 8 | |
| α-helix | 99-102 | 4 | |
| β-strand | 105 | 1 | 10 |
| β-strand | 107 | 1 | 10 |
| β-strand | 110-117 | 8 | 8 |
| β-strand | 134-141 | 8 | 8 |
| β-strand | 150-152 | 3 | 8 |
| β-strand | 156-157 | 2 | 8 |
| α-helix | 159-168 | 10 | |
| β-strand | 179 | 1 | 9 |
| α-helix | 182-187 | 6 | |
| α-helix | 193-201 | 9 | |
| α-helix | 207-261 | 55 | |
| α-helix | 868-877 | 10 | |
| α-helix | 904-944 | 41 | |
| β-strand | 951-956 | 6 | 11 |
| β-strand | 965-970 | 6 | 11 |
| β-strand | 979 | 1 | 11 |
| α-helix | 988-1001 | 14 | |
| β-strand | 1010-1014 | 5 | 9 |
| α-helix | 1023-1036 | 14 | |
| α-helix | 1041-1042 | 2 | |
| β-strand | 1043-1048 | 6 | 9 |
| β-strand | 1061-1063 | 3 | 9 |
| β-strand | 1087 | 1 | 9 |
Chain F: 14 helices, 9 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 14-24 | 11 | |
| α-helix | 29-35 | 7 | |
| β-strand | 45-47 | 3 | 12 |
| α-helix | 48-55 | 8 | |
| α-helix | 60-62 | 3 | |
| α-helix | 69-82 | 14 | |
| β-strand | 88-90 | 3 | 12 |
| β-strand | 122-125 | 4 | 12 |
| α-helix | 133-144 | 12 | |
| α-helix | 147-150 | 4 | |
| β-strand | 151-152 | 2 | 13 |
| β-strand | 155-156 | 2 | 13 |
| β-strand | 200 | 1 | 14 |
| α-helix | 201-208 | 8 | |
| α-helix | 218-220 | 3 | |
| α-helix | 228-236 | 9 | |
| β-strand | 240-242 | 3 | 15 |
| β-strand | 255 | 1 | 14 |
| β-strand | 256-258 | 3 | 15 |
| α-helix | 261-264 | 4 | |
| α-helix | 268-278 | 11 | |
| α-helix | 284-286 | 3 | |
| α-helix | 289-297 | 9 | |
Chain G: 14 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 44-70 | 27 | |
| α-helix | 75-89 | 15 | |
| α-helix | 99-118 | 20 | |
| α-helix | 132-142 | 11 | |
| α-helix | 145-150 | 6 | |
| α-helix | 215-217 | 3 | |
| α-helix | 243-245 | 3 | |
| α-helix | 246-248 | 3 | |
| α-helix | 252-254 | 3 | |
| α-helix | 290-295 | 6 | |
| α-helix | 296-300 | 5 | |
| β-strand | 305-306 | 2 | 16 |
| α-helix | 320-333 | 14 | |
| β-strand | 337-339 | 3 | 16 |
| β-strand | 349-351 | 3 | 16 |
| α-helix | 363-372 | 10 | |
| β-strand | 382-383 | 2 | 9 |
| α-helix | 385-387 | 3 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| DNA (68-mer) | A | DNA | 68 | synthetic construct | |
| DNA (78-mer) | B | DNA | 78 | synthetic construct | |
| Non-structural maintenance of chromosomes element 1 | C | protein | 337 | Saccharomyces cerevisiae W303 | Q07913 (AlphaFold model) |
| Structural maintenance of chromosomes protein 6 | D | protein | 1157 | Saccharomyces cerevisiae W303 | Q12749 (AlphaFold model) |
| Structural maintenance of chromosomes protein 5 | E | protein | 1094 | Saccharomyces cerevisiae W303 | Q08204 (AlphaFold model) |
| Non-structural maintenance of chromosome element 3 | F | protein | 305 | Saccharomyces cerevisiae W303 | Q05541 (AlphaFold model) |
| Non-structural maintenance of chromosome element 4 | G | protein | 403 | Saccharomyces cerevisiae W303 | P43124 |
Sequence of entity 1 (A), FASTA
>7TVE_1 DNA (68-MER) (chains A)
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAA
Sequence of entity 2 (B), FASTA
>7TVE_2 DNA (78-MER) (chains B)
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
TTTTTTTTTTTTTTTTTT
Sequence of entity 3 (C), FASTA
>7TVE_3 Non-structural maintenance of chromosomes element 1 (chains C)
MEVHEEHVSAPVTGDATAKYLLQYILSARGICHENALILALMRLETDASTLNTEWSIQQW
VDKLNDYINAINVKLNLLGYKIIRINHGIGRNAVTLKAKQNFESFEDNTAIRAHDNDYAV
LQSIVLPESNRFFVYVNLASTEETKLATRFNQNEIEFIKWAIEQFMISGETIVEGPALDT
SIIVREVNRILVAATGDSNLAKWRKFSTFTVGSTNLFQFQELTATDIEDLLLRLCELKWF
YRTQEGKFGIDLRCIAELEEYLTSMYNLNTCQNCHKLAIQGVRCGNESCREENEETGENS
LSQIWHVDCFKHYITHVSKNCDRCGSSLITEGVYVIG
Sequence of entity 4 (D), FASTA
>7TVE_4 Structural maintenance of chromosomes protein 6 (chains D)
MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFR
SSSDVATADQDNFLEESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILT
AITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEIIVERIIK
RDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKY
SHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDL
NERKMLLQAKSLWIDVAHNTDACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTT
IEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQAEAQSNIDQGRKKVDALNKT
IAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSLQDVKNEERDIQHERES
ELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLV
TIRKGFEKWTRSIQRAISSSLNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDY
SKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIEDKNEARNFLQRNPVNVNMAL
SLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYE
EKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQA
IASYEAAKEELGLKIEQIAQEAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKY
KDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNACAFCSKERIENVDLPDTQEEI
KRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKAR
DQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLS
GGEKSFSQMALLLATWKPMRSRIIALDQFDVFMDQVNRKIGTTLIVKKLKDIARTQTIII
TPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYNGSLEVLFQGPGGSSAWSHPQFEKGGG
SGGGSGGGSWSHPQFEK
Sequence of entity 5 (E), FASTA
>7TVE_5 Structural maintenance of chromosomes protein 5 (chains E)
MTSLIDLGRYVERTHHGEDTEPRSKRVKIAKPDLSSFQPGSIIKIRLQDFVTYTLTEFNL
SPSLNMIIGPNGSGKSTFVCAVCLGLAGKPEYIGRSKKVEDFIKNGQDVSKIEITLKNSP
NVTDIEYIDARDETIKITRIITRSKRRSDYLINDYQVSESVVKTLVAQLNIQLDNLCQFL
SQERVEEFARLKSVKLLVETIRSIDASLLDVLDELRELQGNEQSLQKDLDFKKAKIVHLR
QESDKLRKSVESLRDFQNKKGEIELHSQLLPYVKVKDHKEKLNIYKEEYERAKANLRAIL
KDKKPFANTKKTLENQVEELTEKCSLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNE
YYRGRTKKLQATIISTKEDFLRSQEILAQTHLPEKSVFEDIDIKRKEIINKEGEIRDLIS
EIDAKANAINHEMRSIQRQAESKTKSLTTTDKIGILNQDQDLKEVRDAVLMVREHPEMKD
KILEPPIMTVSAINAQFAAYLAQCVDYNTSKALTVVDSDSYKLFANPILDKFKVNLRELS
SADTTPPVPAETVRDLGFEGYLSDFITGDKRVMKMLCQTSKIHTIPVSRRELTPAQIKKL
ITPRPNGKILFKRIIHGNRLVDIKQSAYGSKQVFPTDVSIKQTNFYQGSIMSNEQKIRIE
NEIINLKNEYNDRKSTLDALSNQKSGYRHELSELASKNDDINREAHQLNEIRKKYTMRKS
TIETLREKLDQLKREARKDVSQKIKDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQKELI
STQILQFEAQNMDVSMNDVIGFFNEREADLKSQYEDKKKFVKEMRDTPEFQSWMREIRSY
DQDTKEKLNKVAEKYEEEGNFNLSFVQDVLDKLESEIAMVNHDESAVTILDQVTAELREL
EHTVPQQSKDLETIKAKLKEDHAVLEPKLDDIVSKISARFARLFNNVGSAGAVRLEKPKD
YAEWKIEIMVKFRDNAPLKKLDSHTQSGGERAVSTVLYMIALQEFTSAPFRVVDQINQGM
DSRNERIVHKAMVENACAENTSQYFLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPK
MIHFGETSNYSFDG
Sequence of entity 6 (F), FASTA
>7TVE_6 Non-structural maintenance of chromosome element 3 (chains F)
MMSSIDNDSDVDLTEDLAVAKIVKENPVARKMVRYILSRGESQNSIITRNKLQSVIHEAA
REENIAKPSFSKMFMDINAILYNVYGFELQGLPSKNNMNAGGNGSNSNTNKSMPEPLGHR
AQKFILLNNVPHSKNFDDFKILQSAHTYEELIVTGEYIGDDIASGTSNTLESKLSTDRDL
VYKGVLSVILCIVFFSKNNILHQELIKFLETFGIPSDGSKIAILNITIEDLIKSLEKREY
IVRLEEKSDTDGEVISYRIGRRTQAELGLESLEKLVQEIMGLEKEQTKSLHDDIIKSIGD
SYSIG
Sequence of entity 7 (G), FASTA
>7TVE_7 Non-structural maintenance of chromosome element 4 (chains G)
MSSTVISRKRRNSTVTEPDSSGETRKQKKSRSDEKSSSSKDGDPQLEFKVLQGYRDLESE
MHKGRAQVTRTGDIGVAMDNLNAVDSLFNKVIGIKNNGLFAHDARAMVSISELAQISVRN
LKFDDSRSMVNLENIVNSLKRYMLKEHFKLNNIAENRNDLTLAADEQSAADQQEESDGDI
DRTPDDNHTDKATSSFKATSMRHSYLQQFSHYNEFSQFNWFRIGALYNTISKNAPITDHL
MGPLSIEKKPRVLTQRRRNNDQVGEKITAEKITQHSLNSTQQETTPEQVKKCFKKLSKKL
GPEGSINLFKFIIDPNSFSRSIENLFYTSFLIKEGKLLMEHDEEGLPTIKIKQSISHTDS
RSKEIERQRRRAAHQNHIIFQMDMPTWRKLIKKYNITSPFLDG
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ATP | Adenosine-5'-triphosphate | C10 H16 N5 O13 P3 | 1 |
Primary citation
Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes. Yu, Y., Li, S., Ser, Z. et al. Proc Natl Acad Sci U S A (2022) 119:e2202799119-e2202799119. DOI 10.1073/pnas.2202799119 · PubMed
Other PDB entries of the same protein (UniProt Q07913 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 8HQS 3.2 Å, Cryo-EM structure of 8-subunit Smc5/6 head region
- 7YMD 4.18 Å, Cryo-EM structure of Nse1/3/4
- 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
- 7QCD 8.0 Å, CryoEM structure of the Smc5/6-holocomplex (composite structure)
Browse structure collections
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