8I4U: 5-subunit Smc5/6 hinge region

Cryo-EM structure of 5-subunit Smc5/6 hinge region. Determined by electron microscopy at 6.73 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 6.73 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 3
Atoms: 8,963
Mol. weight: 284.83 kDa
Released: 26 Jun 2024

Explore 8I4U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I4U contains 49 α-helices and 27 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: 24 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	332-334	3
α-helix	336-385	50
α-helix	386-388	3
α-helix	396-444	49
α-helix	452-458	7
α-helix	460-473	14
α-helix	476-479	4
β-strand	482-483	2	1
α-helix	486-489	4
β-strand	491	1	2
α-helix	495-498	4
α-helix	499-501	3
α-helix	507-510	4
β-strand	512	1	3
β-strand	514-515	2	1
α-helix	520-524	5
α-helix	526-530	5
β-strand	535	1	3
α-helix	551-553	3
β-strand	560-561	2	4
α-helix	562-565	4
β-strand	567	1	2
α-helix	570-579	10
β-strand	586-587	2	4
α-helix	595-600	6
α-helix	610-612	3
β-strand	613	1	5
β-strand	616	1	5
β-strand	619-623	5	5
β-strand	635-639	5	5
α-helix	640-641	2
α-helix	654-656	3
α-helix	657-662	6
α-helix	663-736	74
α-helix	741-743	3
α-helix	744-767	24

Chain B: 19 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	371-376	6
α-helix	377-415	39
α-helix	420-425	6
α-helix	430-432	3
α-helix	436-479	44
α-helix	482-497	16
α-helix	506-508	3
α-helix	514-524	11
β-strand	540-542	3	6
α-helix	543	1
α-helix	553-556	4
α-helix	569-573	5
β-strand	616-618	3	6
α-helix	621-624	4
α-helix	625-629	5
β-strand	636-641	6	7
α-helix	649-651	3
β-strand	658-662	5	7
β-strand	668-672	5	7
β-strand	676-679	4	7
α-helix	694-697	4
α-helix	698-708	11
α-helix	711-757	47
α-helix	765-768	4
α-helix	771-814	44

Chain C: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	33-48	16
α-helix	60-81	22
α-helix	142-144	3
α-helix	145-148	4
α-helix	150-155	6
β-strand	169	1	8
β-strand	172	1	8
β-strand	183	1	9
β-strand	190	1	9
β-strand	195-196	2	10
β-strand	203-204	2	10
β-strand	217	1	11
β-strand	219	1	11
β-strand	236	1	10
α-helix	240-262	23

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)
E3 SUMO-protein ligase MMS21	C	protein	267	Saccharomyces cerevisiae S288C	P38632 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8I4U_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

>8I4U_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 (C), FASTA

>8I4U_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 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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