8WJL: 6-subunit Smc5/6 hinge region

Cryo-EM structure of 6-subunit Smc5/6 hinge region. Determined by electron microscopy at 6.15 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 6.15 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 3
Atoms: 8,929
Mol. weight: 284.83 kDa
Released: 26 Jun 2024

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

Secondary structure: helices and β-sheets

8WJL contains 48 α-helices and 25 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: 21 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	333-345	13
α-helix	348-384	37
α-helix	397-441	45
α-helix	445-447	3
α-helix	453-458	6
α-helix	460-462	3
α-helix	463-472	10
α-helix	478-481	4
β-strand	482-483	2	5
α-helix	485	1
α-helix	486-489	4
β-strand	492	1	6
α-helix	495-504	10
α-helix	507-510	4
β-strand	514-515	2	5
α-helix	520-523	4
α-helix	547-549	3
β-strand	560-561	2	7
α-helix	562-565	4
β-strand	566	1	6
α-helix	575-577	3
α-helix	582-584	3
β-strand	586-587	2	7
β-strand	603-604	2	8
β-strand	608-609	2	8
β-strand	613-614	2	9
β-strand	621-622	2	9
β-strand	636	1	3
α-helix	660-662	3
α-helix	663-707	45
α-helix	710-765	56
α-helix	768-773	6

Chain B: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	370-376	7
α-helix	377-430	54
α-helix	435-461	27
α-helix	466-490	25
α-helix	491-493	3
α-helix	515-521	7
α-helix	525-527	3
β-strand	541-542	2	1
α-helix	547-552	6
α-helix	554-557	4
α-helix	558-562	5
β-strand	566	1	2
α-helix	569-578	10
α-helix	579-582	4
β-strand	591	1	3
β-strand	592	1	2
β-strand	611	1	4
α-helix	612-615	4
β-strand	616-617	2	1
α-helix	622-630	9
α-helix	633-635	3
β-strand	637-638	2	4
α-helix	647-650	4
β-strand	659-664	6	4
β-strand	667-673	7	4
β-strand	676-680	5	4
β-strand	690	1	1
α-helix	697-700	4
α-helix	703-760	58
α-helix	770-816	47

Chain C: 8 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
α-helix	36-51	16
α-helix	60-80	21
α-helix	138-140	3
α-helix	144-146	3
β-strand	194-196	3	10
β-strand	204-205	2	10
α-helix	232-234	3
α-helix	235	1
β-strand	236-237	2	10
α-helix	242-266	25

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 6	B	protein	1114	Saccharomyces cerevisiae S288C	Q12749 (AlphaFold model)
Structural maintenance of chromosomes protein 5	A	protein	1093	Saccharomyces cerevisiae S288C	Q08204 (AlphaFold model)
E3 SUMO-protein ligase MMS21	C	protein	267	Saccharomyces cerevisiae S288C	P38632 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8WJL_1 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 2 (A), FASTA

>8WJL_2 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 3 (C), FASTA

>8WJL_3 E3 SUMO-protein ligase MMS21 (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) 31:1532-1542. DOI 10.1038/s41594-024-01319-1 · PubMed

Other PDB entries of the same protein (UniProt Q12749 (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
8T8E 3.3 Å, cryoEM structure of Smc5/6 5mer
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
7YLM 6.17 Å, Cryo-EM structure of 8-subunit Smc5/6 hinge region
8I4U 6.73 Å, Cryo-EM structure of 5-subunit Smc5/6 hinge region

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