8WJN: 6-subunit Smc5/6 head region

Cryo-EM structure of 6-subunit Smc5/6 head region. Determined by electron microscopy at 5.58 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 5.58 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 5
Atoms: 14,757
Mol. weight: 373.01 kDa
Released: 26 Jun 2024

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

Secondary structure: helices and β-sheets

8WJN contains 84 α-helices and 48 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 A: 22 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	42-47	6	6
β-strand	57-58	2	6
β-strand	64	1	7
β-strand	66	1	8
α-helix	76-82	7
α-helix	90-92	3
α-helix	99-102	4
β-strand	112-116	5	6
α-helix	120-122	3
β-strand	135-140	6	6
α-helix	148	1
β-strand	149-152	4	6
β-strand	156-157	2	6
α-helix	159-169	11
β-strand	179	1	7
α-helix	182-190	9
α-helix	193-204	12
α-helix	207-260	54
α-helix	270-273	4
α-helix	274-282	9
α-helix	828-832	5
α-helix	834-840	7
α-helix	849-856	8
α-helix	863-869	7
α-helix	871-874	4
α-helix	875-877	3
α-helix	884-947	64
β-strand	950-956	7	9
α-helix	961-963	3
β-strand	965-971	7	9
β-strand	979-980	2	9
α-helix	988-1002	15
β-strand	1010-1013	4	7
α-helix	1023-1036	14
α-helix	1041-1042	2
β-strand	1043-1046	4	7
β-strand	1063	1	8

Chain B: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	82-88	7	1
β-strand	90	1	2
β-strand	95-99	5	1
β-strand	106-108	3	3
α-helix	118-125	8
α-helix	130-133	4
β-strand	143	1	2
β-strand	149-157	9	1
α-helix	166-169	4
β-strand	172-180	9	1
β-strand	188-191	4	1
α-helix	201-210	10
α-helix	218-221	4
α-helix	224-231	8
α-helix	236-246	11
α-helix	249-285	37
α-helix	295-315	21
α-helix	317-320	4
α-helix	874-879	6
α-helix	885-888	4
α-helix	898-917	20
α-helix	922-986	65
β-strand	989-991	3	4
β-strand	994-995	2	5
β-strand	1000-1001	2	5
β-strand	1004-1006	3	4
β-strand	1014-1015	2	4
α-helix	1016-1018	3
α-helix	1021-1036	16
β-strand	1045-1047	3	3
α-helix	1055-1060	6
α-helix	1063-1071	9
β-strand	1078-1081	4	3
α-helix	1085-1088	4
β-strand	1098-1100	3	3

Chain F: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	14-27	14
β-strand	31-33	3	10
α-helix	34-44	11
α-helix	45-47	3
α-helix	57-76	20
β-strand	82-86	5	10
α-helix	91-93	3
α-helix	95-97	3
β-strand	131-135	5	10
α-helix	152-167	16
α-helix	184-194	11
β-strand	207	1	11
α-helix	213-217	5
α-helix	224-236	13
β-strand	241-242	2	12
β-strand	248-249	2	12
α-helix	252-258	7
α-helix	260-265	6
β-strand	282	1	13
α-helix	307-315	9
β-strand	334	1	13
β-strand	335	1	11

Chain G: 14 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-24	13
α-helix	26-41	16
β-strand	46-47	2	14
α-helix	48-61	14
α-helix	69-83	15
β-strand	86-90	5	14
β-strand	122-127	6	14
α-helix	135-150	16
α-helix	152-154	3
α-helix	179-194	16
β-strand	199-200	2	15
α-helix	201-211	11
α-helix	218-220	3
α-helix	227-237	11
β-strand	240-247	8	15
β-strand	251-258	8	15
α-helix	260-265	6
α-helix	268-279	12
α-helix	284-286	3
α-helix	290-297	8

Chain H: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	44-71	28
α-helix	75-90	16
α-helix	100-120	21
α-helix	132-139	8
α-helix	200-205	6
α-helix	220-226	7
α-helix	242-244	3
α-helix	293-300	8
α-helix	308-311	4
α-helix	322-325	4
β-strand	330	1	16
α-helix	331-334	4
α-helix	339-342	4
β-strand	348	1	16
α-helix	361-363	3
α-helix	364-369	6
α-helix	370-372	3
α-helix	388-391	4

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)
Non-structural maintenance of chromosomes element 1	F	protein	336	Saccharomyces cerevisiae S288C	Q07913 (AlphaFold model)
Non-structural maintenance of chromosome element 3	G	protein	303	Saccharomyces cerevisiae S288C	Q05541 (AlphaFold model)
Non-structural maintenance of chromosomes element 4	H	protein	402	Saccharomyces cerevisiae S288C	A0A6L0Z6W9

Sequence of entity 1 (B), FASTA

>8WJN_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

>8WJN_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 (F), FASTA

>8WJN_3 Non-structural maintenance of chromosomes element 1 (chains F)
MEVHEEQVSAPVTGDATAKYLLQYILSARGICHENALILALMRLETDASTLNTEWSIQQW
VDKLNDYINAINVKLNLLGYKIIRINHGIGRNAVTLKAKQNFESFEDNTAIRAHNNDYAV
LQSIVLPESNRFFVYVNLASTEETKLATRFNQNEIEFMKWAIEQFMISGETIVEGPALET
SIIVKEVNRILVAATGDSNLAKWRKFSTFTVGSTNLFQFQELTATDIEDLLLRLCELKWF
YRTQEGKFGIDLRCIAELEEYLTSMYNLNTCQNCHKLAIQGVRCGNESCREENEETGENS
LSQIWHVDCFKHYITHVSKNCDRCGSSLITEGVYVI

Sequence of entity 4 (G), FASTA

>8WJN_4 Non-structural maintenance of chromosome element 3 (chains G)
MSSIDNDSDVDLTEDLAVAKIVKENPVARKMVRYILSRGESQNSIITRNKLQSVIHEAAR
EENIAKPSFSKMFMDINAILYNVYGFELQGLPSKNNMNAGGNGSNSNTNKSMPEPLGHRA
QKFILLNNVPHSKNFDDFKILQSAHTYEELIVTGEYIGDDIASGTSNTLESKLSTDRDLV
YKGVLSVILCIVFFSKNNILHQELIKFLETFGIPSDGSKIAILNITIEDLIKSLEKREYI
VRLEEKSDTDGEVISYRIGRRTQAELGLESLEKLVQEIMGLEKEQTKSLHDDIIKSIGDS
YSI

Sequence of entity 5 (H), FASTA

>8WJN_5 Non-structural maintenance of chromosomes 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 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
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
8I4U 6.73 Å, Cryo-EM structure of 5-subunit Smc5/6 hinge region

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