8I4W: 5-subunit Smc5/6 head region

Cryo-EM structure of 5-subunit Smc5/6 head region. Determined by electron microscopy at 6.01 Å resolution. Released 26 Jun 2024.

Method: Electron microscopy
Resolution: 6.01 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 4
Atoms: 14,037
Mol. weight: 372.35 kDa
Released: 26 Jun 2024

Explore 8I4W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8I4W contains 90 α-helices and 39 β-strands across 4 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: 18 helices, 14 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	207-253	47
α-helix	891-909	19
α-helix	913-944	32
β-strand	953-956	4	4
α-helix	961-963	3
β-strand	965-968	4	4
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: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	13-35	23
α-helix	77-78	2
β-strand	82-88	7	5
β-strand	90	1	6
β-strand	96-98	3	5
β-strand	104-107	4	7
α-helix	109-110	2
α-helix	117-126	10
α-helix	130-133	4
α-helix	139-142	4
β-strand	143	1	6
α-helix	144	1
β-strand	149-157	9	5
α-helix	166-169	4
β-strand	172-180	9	5
β-strand	186-188	3	5
β-strand	190	1	8
β-strand	196	1	8
α-helix	202-211	10
β-strand	221-222	2	7
α-helix	224-231	8
α-helix	236-246	11
α-helix	250-297	48
α-helix	915-918	4
α-helix	922-983	62
α-helix	984-986	3
β-strand	989-995	7	9
β-strand	1000-1006	7	9
β-strand	1014-1015	2	9
α-helix	1021-1036	16
β-strand	1043-1046	4	7
α-helix	1056-1070	15
β-strand	1076-1080	5	7
α-helix	1085-1087	3
β-strand	1096-1099	4	7

Chain D: 20 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	143-150	8
α-helix	164-172	9
α-helix	182-189	8
β-strand	198-199	2	10
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	10
β-strand	281	1	11
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	12
β-strand	22	1	12
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	13
β-strand	202	1	13
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	11
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	1093	Saccharomyces cerevisiae S288C	Q08204 (AlphaFold model)
Structural maintenance of chromosomes protein 6	B	protein	1114	Saccharomyces cerevisiae S288C	Q12749 (AlphaFold model)
DNA repair protein KRE29	D	protein	464	Saccharomyces cerevisiae S288C	P40026 (AlphaFold model)
Non-structural maintenance of chromosome element 5	E	protein	556	Saccharomyces cerevisiae S288C	Q03718 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8I4W_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

>8I4W_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 (D), FASTA

>8I4W_3 DNA repair protein KRE29 (chains D)
MGSVNSSPNEEFETVPDSQISGFDSPLIPTSVGSYFRDDDDDEKVHPNFISDPENDSLNS
DEEFSSLENSDLNLSGAKAESGDDFDPILKRTIISKRKAPSNNEDEEIVKTPRKLVNYVP
LKIFNLGDSFDDTITTTVAKLQDLKKEILDSPRSNKSIVITSNTVAKSELQKSIKFSGSI
PEIYLDVVTKETISDKYKDWHFISKNCHYEQLMDLEMKDTAYSFLFGSSRSQGKVPEFVH
LKCPSITNLLVLFGVNQEKCNSLKINYEKKENSRYDNLCTIFPVNKMLKFLMYFYSDDDN
DDVREFFLKAFICLILDRKVFNAMESDHRLCFKVLELFNEAHFINSYFEIVDKNDFFLHY
RLLQIFPHLQSALLRRRFSEKQGRTETIQQNIIKEFNEFFDCKNYKNLLYFILTMYGSKF
IPFGPKCQVTEYFKDCILDISNETTNDVEISILKGILNLFSKIR

Sequence of entity 4 (E), FASTA

>8I4W_4 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
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

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