7QCD: Smc5/6-holocomplex

CryoEM structure of the Smc5/6-holocomplex (composite structure). Determined by electron microscopy at 8.0 Å resolution. Released 21 Sept 2022.

Method: Electron microscopy
Resolution: 8.0 Å
Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 6
Atoms: 25,133
Mol. weight: 442.84 kDa
Ligands: ZN
Released: 21 Sept 2022

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

Secondary structure: helices and β-sheets

7QCD contains 125 α-helices and 95 β-strands across 6 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: 39 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	41-42	2	1
β-strand	45-50	6	1
β-strand	53-59	7	1
β-strand	68	1	2
α-helix	75-84	10
α-helix	90-92	3
α-helix	99-102	4
β-strand	103	1	1
α-helix	104	1
β-strand	109-117	9	1
β-strand	125	1	3
β-strand	128	1	3
β-strand	134-142	9	1
α-helix	148	1
β-strand	149	1	1
β-strand	150-151	2	4
β-strand	152	1	1
β-strand	156-157	2	4
α-helix	159-168	10
α-helix	182-188	7
α-helix	193-204	12
α-helix	207-269	63
α-helix	271-359	89
α-helix	361-365	5
α-helix	374-389	16
α-helix	395-445	51
α-helix	452-455	4
α-helix	456-458	3
α-helix	460-474	15
α-helix	477-480	4
β-strand	482	1	5
α-helix	486-489	4
β-strand	491-492	2	6
α-helix	495-504	10
α-helix	507-510	4
β-strand	513-515	3	5
α-helix	518-525	8
β-strand	536-538	3	5
α-helix	550-554	5
β-strand	560-561	2	7
β-strand	566-567	2	6
α-helix	570-575	6
α-helix	576-580	5
α-helix	582-584	3
β-strand	586-587	2	7
α-helix	591-593	3
α-helix	594-601	8
α-helix	603-604	2
β-strand	614-616	3	7
β-strand	619-621	3	7
β-strand	624-625	2	8
β-strand	633-634	2	8
β-strand	637-639	3	7
α-helix	653-721	69
α-helix	722-728	7
α-helix	729-737	9
α-helix	741-824	84
α-helix	828-839	12
α-helix	842-858	17
α-helix	863-878	16
α-helix	885-947	63
β-strand	950-956	7	9
α-helix	961-963	3
β-strand	965-971	7	9
β-strand	979-981	3	9
α-helix	988-1005	18
β-strand	1010-1013	4	10
α-helix	1022-1037	16
β-strand	1043-1046	4	10
β-strand	1048	1	2

Chain B: 34 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	75-77	3
β-strand	78	1	11
β-strand	81-82	2	12
β-strand	84-86	3	13
β-strand	87-88	2	14
β-strand	90	1	15
β-strand	93	1	15
β-strand	97-99	3	13
β-strand	105-108	4	16
α-helix	115-124	10
α-helix	130-132	3
β-strand	150-155	6	14
β-strand	156-157	2	12
β-strand	161	1	11
β-strand	174-179	6	14
α-helix	185	1
β-strand	186-190	5	14
β-strand	196-198	3	14
α-helix	201-211	11
α-helix	224-231	8
α-helix	236-246	11
α-helix	249-288	40
α-helix	293-368	76
α-helix	388-430	43
α-helix	437-500	64
α-helix	506-509	4
α-helix	514-523	10
α-helix	536-539	4
β-strand	540-542	3	17
α-helix	550-559	10
β-strand	564-565	2	18
α-helix	569-582	14
β-strand	590-591	2	18
α-helix	601-603	3
β-strand	606	1	19
α-helix	610	1
β-strand	611	1	20
β-strand	616-618	3	17
α-helix	621-631	11
α-helix	633-635	3
β-strand	637	1	20
α-helix	642-651	10
β-strand	654	1	19
β-strand	659-662	4	21
β-strand	667-672	6	21
β-strand	676-681	6	21
α-helix	682-683	2
β-strand	690	1	17
α-helix	695-756	62
α-helix	757-759	3
α-helix	767-800	34
α-helix	815-880	66
α-helix	885-888	4
α-helix	897-917	21
α-helix	923-985	63
β-strand	989-995	7	22
β-strand	1000-1006	7	22
β-strand	1013-1015	3	22
α-helix	1016-1018	3
α-helix	1021-1036	16
β-strand	1043-1046	4	16
α-helix	1050-1052	3
α-helix	1055-1068	14
β-strand	1076-1081	6	16
α-helix	1085-1088	4

Chain C: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	16-23	8
α-helix	31-51	21
α-helix	60-100	41
α-helix	106-113	8
α-helix	122-128	7
α-helix	130-132	3
α-helix	142-155	14
α-helix	172-177	6
β-strand	183	1	23
β-strand	190	1	23
β-strand	195-197	3	24
β-strand	203-204	2	24
α-helix	206-212	7
β-strand	219-220	2	25
β-strand	229-230	2	25
β-strand	235-237	3	24
α-helix	239-265	27

Chain D: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	12-27	16
β-strand	31-33	3	26
α-helix	34-48	15
α-helix	57-77	21
β-strand	80-86	7	26
α-helix	90-109	20
α-helix	116-123	8
α-helix	125-128	4
β-strand	131-137	7	26
α-helix	142-145	4
α-helix	152-170	19
β-strand	173-174	2	27
α-helix	182-195	14
α-helix	200-203	4
β-strand	205-207	3	27
α-helix	213-216	4
α-helix	224-236	13
β-strand	240-242	3	28
β-strand	248-250	3	28
α-helix	252-266	15
β-strand	281-284	4	27
α-helix	287-290	4
β-strand	293	1	29
β-strand	298	1	29
α-helix	301-303	3
β-strand	304-305	2	27
α-helix	307-316	10
β-strand	320	1	30
β-strand	327	1	30
β-strand	332-335	4	27

Chain E: 15 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	27-42	16
β-strand	46-47	2	31
α-helix	48-62	15
α-helix	69-82	14
β-strand	86-91	6	31
α-helix	92-93	2
α-helix	95-98	4
α-helix	117-119	3
β-strand	122-127	6	31
α-helix	133-150	18
α-helix	174-194	21
β-strand	199-200	2	32
α-helix	201-210	10
α-helix	218-220	3
α-helix	227-236	10
β-strand	240-247	8	32
β-strand	251-258	8	32
α-helix	260-265	6
α-helix	268-278	11
α-helix	286-297	12

Chain F: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	44-70	27
α-helix	75-91	17
α-helix	97-122	26
α-helix	185-196	12
α-helix	217-230	14
α-helix	234-235	2
β-strand	241	1	33
β-strand	244	1	33
α-helix	285-300	16
β-strand	306-307	2	34
α-helix	308-312	5
α-helix	318-332	15
β-strand	338-341	4	34
β-strand	347-350	4	34
α-helix	360-372	13
β-strand	376-378	3	1
α-helix	384-394	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Structural maintenance of chromosomes protein 5	A	protein	1093	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q08204 (AlphaFold model)
Structural maintenance of chromosomes protein 6	B	protein	1114	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q12749 (AlphaFold model)
E3 SUMO-protein ligase MMS21	C	protein	281	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P38632 (AlphaFold model)
Non-structural maintenance of chromosomes element 1	D	protein	358	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q07913 (AlphaFold model)
Non-structural maintenance of chromosome element 3	E	protein	303	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Q05541
Non-structural maintenance of chromosome element 4	F	protein	715	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P43124

Sequence of entity 1 (A), FASTA

>7QCD_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
YAEWKIEIMVKFRDNAPLKKLDSHTQSGGERAVSTVLYMIALQEFTSAPFRVVDQINQGM
DSRNERIVHKAMVENACAENTSQYFLITPKLLTGLHYHEKMRIHCVMAGSWIPNPSEDPK
MIHFGETSNYSFD

Sequence of entity 2 (B), FASTA

>7QCD_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
GGEKSFSQMALLLATWKPMRSRIIALDQFDVFMDQVNRKIGTTLIVKKLKDIARTQTIII
TPQDIGKIADIDSSGVSIHRMRDPERQNNSNFYN

Sequence of entity 3 (C), FASTA

>7QCD_3 E3 SUMO-protein ligase MMS21 (chains C)
MGSYPYDVPDYAGSGALNDNPIPKSVPLHPKSGKYFHNLHARDLSNIYQQCYKQIDETIN
QLVDSTSPSTIGIEEQVADITSTYKLLSTYESESNSFDEHIKDLKKNFKQSSDACPQIDL
STWDKYRTGELTAPKLSELYLNMPTPEPATMVNNTDTLKILKVLPYIWNDPTCVIPDLQN
PADEDDLQIEGGKIELTCPITCKPYEAPLISRKCNHVFDRDGIQNYLQGYTTRDCPQAAC
SQVVSMRDFVRDPIMELRCKIAKMKESQEQDKRSSQAIDVL

Sequence of entity 4 (D), FASTA

>7QCD_4 Non-structural maintenance of chromosomes element 1 (chains D)
MGSSHHHHHHSSGRENLYFQGHMEVHEEQVSAPVTGDATAKYLLQYILSARGICHENALI
LALMRLETDASTLNTEWSIQQWVDKLNDYINAINVKLNLLGYKIIRINHGIGRNAVTLKA
KQNFESFEDNTAIRAHNNDYAVLQSIVLPESNRFFVYVNLASTEETKLATRFNQNEIEFM
KWAIEQFMISGETIVEGPALETSIIVKEVNRILVAATGDSNLAKWRKFSTFTVGSTNLFQ
FQELTATDIEDLLLRLCELKWFYRTQEGKFGIDLRCIAELEEYLTSMYNLNTCQNCHKLA
IQGVRCGNESCREENEETGENSLSQIWHVDCFKHYITHVSKNCDRCGSSLITEGVYVI

Sequence of entity 5 (E), FASTA

>7QCD_5 Non-structural maintenance of chromosome element 3 (chains E)
MSSIDNDSDVDLTEDLAVAKIVKENPVARKMVRYILSRGESQNSIITRNKLQSVIHEAAR
EENIAKPSFSKMFMDINAILYNVYGFELQGLPSKNNMNAGGNGSNSNTNKSMPEPLGHRA
QKFILLNNVPHSKNFDDFKILQSAHTYEELIVTGEYIGDDIASGTSNTLESKLSTDRDLV
YKGVLSVILCIVFFSKNNILHQELIKFLETFGIPSDGSKIAILNITIEDLIKSLEKREYI
VRLEEKSDTDGEVISYRIGRRTQAELGLESLEKLVQEIMGLEKEQTKSLHDDIIKSIGDS
YSI

Sequence of entity 6 (F), FASTA

>7QCD_6 Non-structural maintenance of chromosome element 4 (chains F)
MSSTVISRKRRNSTVTEPDSSGETRKQKKSRSDEKSSSSKDGDPQLEFKVLQGYRDLESE
MHKGRAQVTRTGDIGVAMDNLNAVDSLFNKVIGIKNNGLFAHDARAMVSISELAQISVRN
LKFDDSRSMVNLENIVNSLKRYMLKEHFKLNNIAENRNDLTLAADEQSAADQQEESDGDI
DRTPDDNHTDKATSSFKATSMRHSYLQQFSHYNEFSQFNWFRIGALYNTISKNAPITDHL
MGPLSIEKKPRVLTQRRRNNDQVGEKITAEKITQHSLNSTQQETTPEQVKKCFKKLSKKL
GPEGSINLFKFIIDPNSFSRSIENLFYTSFLIKEGKLLMEHDEEGLPTIKIKQSISHTDS
RSKEIERQRRRAAHQNHIIFQMDMPTWRKLIKKYNITSPFLDGSSGMAEIGTGFPFDPHY
VEVLGERMHYVDVGPRDGTPVLFLHGNPTSSYVWRNIIPHVAPTHRCIAPDLIGMGKSDK
PDLGYFFDDHVRFMDAFIEALGLEEVVLVIHDWGSALGFHWAKRNPERVKGIAFMEFIRP
IPTWDEWPEFARETFQAFRTTDVGRKLIIDQNVFIEGTLPMGVVRPLTEVEMDHYREPFL
NPVDREPLWRFPNELPIAGEPANIVALVEEYMDWLHQSPVPKLLFWGTPGVLIPPAEAAR
LAKSLPNCKAVDIGPGLNLLQEDNPDLIGSEIARWLSTLEISGGSEQKLISEEDL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3

Primary citation

Cryo-EM structure of the Smc5/6 holo-complex. Hallett, S.T., Campbell Harry, I., Schellenberger, P. et al. Nucleic Acids Res (2022) 50:9505-9520. DOI 10.1093/nar/gkac692 · 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

Browse structure collections

About this viewer

MolViewer shows 7QCD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.