7YLM: 8-subunit Smc5/6 hinge region

Cryo-EM structure of 8-subunit Smc5/6 hinge region. Determined by electron microscopy at 6.17 Å resolution. Released 31 Jan 2024.

Method: Electron microscopy
Resolution: 6.17 Å
Organism: Saccharomyces cerevisiae
Chains: 3
Atoms: 8,289
Mol. weight: 284.83 kDa
Released: 31 Jan 2024

Explore 7YLM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7YLM contains 42 α-helices and 23 β-strands across 3 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: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	349-352	4
α-helix	353-356	4
α-helix	357-359	3
α-helix	360-363	4
α-helix	365-388	24
α-helix	397-446	50
α-helix	453-458	6
α-helix	462-474	13
α-helix	486-488	3
β-strand	490	1	1
α-helix	495-502	8
α-helix	507-510	4
β-strand	512-514	3	2
α-helix	523-525	3
β-strand	535-537	3	2
β-strand	568	1	1
α-helix	570-580	11
α-helix	582-584	3
α-helix	594-597	4
α-helix	598-600	3
β-strand	613-616	4	3
β-strand	619-623	5	3
β-strand	635-639	5	3
α-helix	659-754	96
α-helix	755-757	3
α-helix	758-761	4
β-strand	764	1	4
β-strand	766	1	4

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	390-424	35
α-helix	429-486	58
α-helix	489-492	4
α-helix	495-497	3
β-strand	509	1	5
β-strand	511	1	5
α-helix	515-518	4
α-helix	538-540	3
α-helix	552-557	6
α-helix	558-560	3
β-strand	564	1	6
α-helix	572-578	7
β-strand	581	1	7
β-strand	583	1	7
β-strand	589	1	3
β-strand	590	1	6
α-helix	621-624	4
β-strand	661-662	2	8
β-strand	670-671	2	8
α-helix	703-757	55
α-helix	764-785	22
α-helix	788-802	15
α-helix	805-812	8

Chain C: 9 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	44-51	8
α-helix	65-67	3
α-helix	142-147	6
α-helix	150-154	5
β-strand	184	1	9
β-strand	188	1	9
α-helix	189-191	3
β-strand	194-196	3	10
β-strand	203-205	3	10
α-helix	206-212	7
α-helix	232-234	3
β-strand	236	1	10
α-helix	242-252	11
α-helix	255-264	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 5	A	protein	1093	Saccharomyces cerevisiae	Q08204 (AlphaFold model)
SMC6 isoform 1	B	protein	1114	Saccharomyces cerevisiae	Q12749 (AlphaFold model)
MMS21 isoform 1	C	protein	267	Saccharomyces cerevisiae	P38632 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YLM_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

>7YLM_2 SMC6 isoform 1 (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 (C), FASTA

>7YLM_3 MMS21 isoform 1 (chains C)
MALNDNPIPKSVPLHPKSGKYFHNLHARDLSNIYQQCYKQIDETINQLVDSTSPSTIGIE
EQVADITSTYKLLSTYESESNSFDEHIKDLKKNFKQSSDACPQIDLSTWDKYRTGELTAP
KLSELYLNMPTPEPATMVNNTDTLKILKVLPYIWNDPTCVIPDLQNPADEDDLQIEGGKI
ELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPI
MELRCKIAKMKESQEQDKRSSQAIDVL

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). 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
8HQS 3.2 Å, Cryo-EM structure of 8-subunit Smc5/6 head region
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

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