8I4X: 5-subunit Smc5/6

Cryo-EM structure of 5-subunit Smc5/6. Determined by electron microscopy at 8.5 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 8.5 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 5
Atoms: 26,724
Mol. weight: 389.25 kDa
Released: 26 Jun 2024

Explore 8I4X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I4X contains 151 α-helices and 65 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: 47 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	29-31	3
α-helix	38	1
β-strand	42-50	9	1
β-strand	53-59	7	1
β-strand	65-68	4	2
α-helix	75-85	11
α-helix	90-93	4
α-helix	99-102	4
α-helix	104	1
β-strand	109-117	9	1
β-strand	134-142	9	1
β-strand	149-152	4	1
β-strand	155-158	4	1
α-helix	159-168	10
β-strand	179-180	2	3
α-helix	182-189	8
α-helix	193-203	11
α-helix	207-267	61
α-helix	272-388	117
α-helix	392-394	3
α-helix	397-444	48
α-helix	455-457	3
α-helix	460-474	15
α-helix	476-478	3
β-strand	482-483	2	4
α-helix	484-485	2
α-helix	486-489	4
β-strand	491-492	2	5
α-helix	495-504	10
α-helix	507-510	4
α-helix	512	1
β-strand	513-515	3	4
α-helix	518-531	14
β-strand	536-538	3	4
α-helix	550-555	6
β-strand	560-561	2	6
α-helix	562-565	4
β-strand	566-567	2	5
α-helix	570-580	11
α-helix	582-584	3
β-strand	586-588	3	6
α-helix	591-593	3
α-helix	594-601	8
α-helix	603-604	2
β-strand	613-616	4	6
β-strand	619-625	7	6
β-strand	633-639	7	6
α-helix	640-642	3
α-helix	654-656	3
α-helix	657-661	5
α-helix	662-768	107
α-helix	771-780	10
α-helix	783-824	42
α-helix	828-832	5
α-helix	836-842	7
α-helix	847-862	16
α-helix	867-881	15
α-helix	891-909	19
α-helix	913-944	32
β-strand	953-956	4	7
α-helix	961-963	3
β-strand	965-968	4	7
α-helix	977	1
α-helix	988-1001	14
β-strand	1012-1013	2	3
α-helix	1024-1037	14
β-strand	1045	1	2
β-strand	1062-1065	4	2
α-helix	1073-1074	2
α-helix	1079-1081	3
β-strand	1083	1	1

Chain B: 36 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	13-35	23
α-helix	77-78	2
β-strand	82-88	7	8
β-strand	90	1	9
β-strand	96-98	3	8
β-strand	104-107	4	10
α-helix	109-110	2
α-helix	117-126	10
α-helix	130-133	4
α-helix	139-142	4
β-strand	143	1	9
α-helix	144	1
β-strand	149-157	9	8
α-helix	166-169	4
β-strand	172-180	9	8
β-strand	186-188	3	8
β-strand	190	1	11
β-strand	196	1	11
α-helix	202-211	10
β-strand	221-222	2	10
α-helix	224-231	8
α-helix	236-246	11
α-helix	250-425	176
α-helix	429-497	69
α-helix	506-509	4
α-helix	514-523	10
α-helix	525-527	3
β-strand	533	1	6
α-helix	536-539	4
β-strand	540-542	3	12
α-helix	543	1
α-helix	547-549	3
α-helix	550-556	7
α-helix	558-561	4
β-strand	564-566	3	6
α-helix	569-582	14
β-strand	590-592	3	6
α-helix	601-603	3
β-strand	611	1	13
α-helix	612-615	4
β-strand	616-618	3	12
α-helix	621-631	11
α-helix	633-635	3
β-strand	636-638	3	13
α-helix	642-650	9
β-strand	658-662	5	13
β-strand	667-672	6	13
β-strand	676-681	6	13
α-helix	682-683	2
β-strand	689-690	2	12
α-helix	694-758	65
α-helix	765-881	117
α-helix	897-918	22
α-helix	922-983	62
α-helix	984-986	3
β-strand	989-995	7	14
β-strand	1000-1006	7	14
β-strand	1014-1015	2	14
α-helix	1021-1036	16
β-strand	1043-1046	4	10
α-helix	1056-1070	15
β-strand	1076-1080	5	10
α-helix	1085-1087	3
β-strand	1096-1099	4	10

Chain C: 11 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	16-24	9
α-helix	27-29	3
α-helix	31-51	21
α-helix	60-100	41
α-helix	102-104	3
α-helix	108-114	7
α-helix	122-128	7
α-helix	130-132	3
α-helix	142-155	14
β-strand	195-197	3	15
β-strand	203-204	2	15
α-helix	209-213	5
β-strand	219-220	2	16
β-strand	229-230	2	16
β-strand	235-237	3	15
α-helix	239-266	28

Chain D: 23 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	88-93	6
α-helix	104-105	2
α-helix	110-112	3
α-helix	132-150	19
α-helix	164-172	9
α-helix	182-189	8
β-strand	198-199	2	17
α-helix	209-220	12
α-helix	227-229	3
α-helix	236-242	7
α-helix	246-253	8
α-helix	257-261	5
β-strand	274-275	2	17
β-strand	281	1	18
α-helix	284-292	9
α-helix	301-315	15
α-helix	318-323	6
α-helix	329-337	9
α-helix	340-350	11
α-helix	356-365	10
α-helix	367-369	3
α-helix	370-377	8
α-helix	388-402	15
α-helix	405-415	11
α-helix	428-440	13
α-helix	448-462	15

Chain E: 34 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	19
β-strand	22	1	19
α-helix	26-40	15
α-helix	44-53	10
α-helix	62-65	4
α-helix	66-76	11
α-helix	80-90	11
α-helix	100-116	17
α-helix	125-141	17
α-helix	143-147	5
α-helix	191-193	3
β-strand	197	1	20
β-strand	202	1	20
α-helix	204-208	5
α-helix	214-225	12
α-helix	230-234	5
α-helix	235-240	6
α-helix	241-257	17
α-helix	258-262	5
α-helix	271-277	7
α-helix	280-286	7
α-helix	293-301	9
α-helix	308-309	2
α-helix	310-312	3
α-helix	313-317	5
β-strand	336	1	18
α-helix	340-363	24
α-helix	366	1
α-helix	378-390	13
α-helix	395-402	8
α-helix	414-429	16
α-helix	438-441	4
α-helix	445-457	13
α-helix	463-464	2
α-helix	472-497	26
α-helix	506-527	22
α-helix	534-536	3
α-helix	539-542	4
α-helix	543-547	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 5	A	protein	1069	Saccharomyces cerevisiae S288C	Q08204 (AlphaFold model)
Structural maintenance of chromosomes protein 6	B	protein	1104	Saccharomyces cerevisiae S288C	Q12749 (AlphaFold model)
E3 SUMO-protein ligase MMS21	C	protein	267	Saccharomyces cerevisiae S288C	P38632 (AlphaFold model)
Nse6	D	protein	378	Saccharomyces cerevisiae S288C	P40026 (AlphaFold model)
Non-structural maintenance of chromosome element 5	E	protein	556	Saccharomyces cerevisiae S288C	Q03718

Sequence of entity 1 (A), FASTA

>8I4X_1 Structural maintenance of chromosomes protein 5 (chains A)
KRVKIAKPDLSSFQPGSIIKIRLQDFVTYTLTEFNLSPSLNMIIGPNGSGKSTFVCAVCL
GLAGKPEYIGRSKKVEDFIKNGQDVSKIEITLKNSPNVTDIEYIDARDETIKITRIITRS
KRRSDYLINDYQVSESVVKTLVAQLNIQLDNLCQFLSQERVEEFARLKSVKLLVETIRSI
DASLLDVLDELRELQGNEQSLQKDLDFKKAKIVHLRQESDKLRKSVESLRDFQNKKGEIE
LHSQLLPYVKVKDHKEKLNIYKEEYERAKANLRAILKDKKPFANTKKTLENQVEELTEKC
SLKTDEFLKAKEKINEIFEKLNTIRDEVIKKKNQNEYYRGRTKKLQATIISTKEDFLRSQ
EILAQTHLPEKSVFEDIDIKRKEIINKEGEIRDLISEIDAKANAINHEMRSIQRQAESKT
KSLTTTDKIGILNQDQDLKEVRDAVLMVREHPEMKDKILEPPIMTVSAINAQFAAYLAQC
VDYNTSKALTVVDSDSYKLFANPILDKFKVNLRELSSADTTPPVPAETVRDLGFEGYLSD
FITGDKRVMKMLCQTSKIHTIPVSRRELTPAQIKKLITPRPNGKILFKRIIHGNRLVDIK
QSAYGSKQVFPTDVSIKQTNFYQGSIMSNEQKIRIENEIINLKNEYNDRKSTLDALSNQK
SGYRHELSELASKNDDINREAHQLNEIRKKYTMRKSTIETLREKLDQLKREARKDVSQKI
KDIDDQIQQLLLKQRHLLSKMASSMKSLKNCQKELISTQILQFEAQNMDVSMNDVIGFFN
EREADLKSQYEDKKKFVKEARDTPEFQSWMREIRSYDQDTKEKLNKVAEKYEEEGNFNLS
FVQDVLDKLESEIAMVNHDESAVTILDQVTAELRELEHTVPQQSKDLETIKAKLKEDHAV
LEPKLDDIVSKISARFARLFNNVGSAGAVRLEKPKDYAEWKIEIMVKFRDNAPLKKLDSH
TQSGGERAVSTVLYMIALQEFTSAPFRVVDEINQGMDSRNERIVHKAMVENACAENTSQY
FLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPKMIHFGETSNYSFD

Sequence of entity 2 (B), FASTA

>8I4X_2 Structural maintenance of chromosomes protein 6 (chains B)
MISTTISGKRPIEQVDDELLSLTAQQENEEQQQQRKRRRHQFAPMTQFNSNTLDEDSGFR
SSSDVATADQDNFLEESPSGYIKKVILRNFMCHEHFELELGSRLNFIVGNNGSGKSAILT
AITIGLGAKASETNRGSSLKDLIREGCYSAKIILHLDNSKYGAYQQGIFGNEIIVERIIK
RDGPASFSLRSENGKEISNKKKDIQTVVDYFSVPVSNPMCFLSQDAARSFLTASTSQDKY
SHFMKGTLLQEITENLLYASAIHDSAQENMALHLENLKSLKAEYEDAKKLLRELNQTSDL
NERKMLLQAKSLWIDVAHNTDACKNLENEISGIQQKVDEVTEKIRNRQEKIERYTSDGTT
IEAQIDAKVIYVNEKDSEHQNARELLRDVKSRFEKEKSNQAEAQSNIDQGRKKVDALNKT
IAHLEEELTKEMGGDKDQMRQELEQLEKANEKLREVNNSLVVSAQDVKNEERDIQHERES
ELRTISRSIQNKKVELQNIAKGNDTFLMNFDRNMDRLLRTIEQRKNEFETPAIGPLGSLV
TIRKGFEKWTRSIQRAISSSLNAFVVSNPKDNRLFRDIMRSCGIRSNIPIVTYCLSQFDY
SKGRAHGNYPTIVDALEFSKPEIECLFVDLSRIERIVLIEDKNEARNFLQRNPVNVNMAL
SLRDRRSGFQLSGGYRLDTVTYQDKIRLKVNSSSDNGTQYLKDLIEQETKELQNIRDRYE
EKLSEVRSRLKEIDGRLKSTKNEMRKTNFRMTELKMNVGKVVDTGILNSKINERKNQEQA
IASYEAAKEELGLKIEQIAQEAQPIKEQYDSTKLALVEAQDELQQLKEDINSRQSKIQKY
KDDTIYYEDKKKVYLENIKKIEVNVAALKEGIQRQIQNACAFCSKERIENVDLPDTQEEI
KRELDKVSRMIQKAEKSLGLSQEEVIALFEKCRNKYKEGQKKYMEIDEALNRLHNSLKAR
DQNYKNAEKGTCFDADMDFRASLKVRKFSGNLSFIKDTKSLEIYILTTNDEKARNVDTLS
GGEKSFSQMALLLATWKPMRSRIIALDEFDVFMDQVNRKIGTTLIVKKLKDIARTQTIII
TPQDIGKIADIDSSGVSIHRMRDP

Sequence of entity 3 (C), FASTA

>8I4X_3 E3 SUMO-protein ligase MMS21 (chains C)
MALNDNPIPKSVPLHPKSGKYFHNLHARDLSNIYQQCYKQIDETINQLVDSTSPSTIGIE
EQVADITSTYKLLSTYESESNSFDEHIKDLKKNFKQSSDACPQIDLSTWDKYRTGELTAP
KLSELYLNMPTPEPATMVNNTDTLKILKVLPYIWNDPTCVIPDLQNPADEDDLQIEGGKI
ELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAACSQVVSMRDFVRDPI
MELRCKIAKMKESQEQDKRSSQAIDVL

Sequence of entity 4 (D), FASTA

>8I4X_4 Nse6 (chains D)
PILKRTIISKRKAPSNNEDEEIVKTPRKLVNYVPLKIFNLGDSFDDTITTTVAKLQDLKK
EILDSPRSNKSIVITSNTVAKSELQKSIKFSGSIPEIYLDVVTKETISDKYKDWHFISKN
CHYEQLMDLEMKDTAYSFLFGSSRSQGKVPEFVHLKCPSITNLLVLFGVNQEKCNSLKIN
YEKKENSRYDNLCTIFPVNKMLKFLMYFYSDDDNDDVREFFLKAFICLILDRKVFNAMES
DHRLCFKVLELFNEAHFINSYFEIVDKNDFFLHYRLLQIFPHLQSALLRRRFSEKQGRTE
TIQQNIIKEFNEFFDCKNYKNLLYFILTMYGSKFIPFGPKCQVTEYFKDCILDISNETTN
DVEISILKGILNLFSKIR

Sequence of entity 5 (E), FASTA

>8I4X_5 Non-structural maintenance of chromosome element 5 (chains E)
MDGALINSVLYVSPRNGAHYFVELTEKHLLAFEMLNSMCLLENYDHVLLFLECQFGKSHN
LAVIPFDIILVLFTLSTLSEYYKEPILRANDPYNTSRETLSRRALKLLQKYLAILKEFDS
EQYNLYDLELLRCQFFLAIDTLTPKKQKWGFDRFRRTKSESGVTYRQNASVDPELDQAKT
FKNPYRSYISCLEQRNTILGNRLLNLKLNEPGEFINMILWTLSNSLQESTPLFLSSHEIW
MPLLEILIDLFSCRQDYFIQHEVAQNVSKSLFVQRLSESPLAVFFESLNTRNFANRFSEY
VFLNCDYKLPSDNYATPVHPVYNGENTIVDTYIPTIKCSPLYKSQKSLALRRKLIGSCFK
LLLRVPDGHRLITPRIVADDVIQGISRTLASFNDILQFKKFFMTENLSQESYFIPLLAEG
TLSEILKDTQECVVILTLVENLSDGVSFCNEVIGLVKSKCFAFTEQCSQASYEEAVLNIE
KCDVCLLVLLRYLLHLIGTEAILDAKEQLEMLHAIEKNDSGRRQWAKALNLGNDPPLLYP
IVSQMFGVHDKSVIIE

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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