7YMD: Nse1/3/4

Cryo-EM structure of Nse1/3/4. Determined by electron microscopy at 4.18 Å resolution. Released 31 Jan 2024.

Method: Electron microscopy
Resolution: 4.18 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 3
Atoms: 5,653
Mol. weight: 118.57 kDa
Released: 31 Jan 2024

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

Secondary structure: helices and β-sheets

7YMD contains 38 α-helices and 23 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	115-120	6
α-helix	132-139	8
α-helix	153-155	3
α-helix	200-205	6
α-helix	207-210	4
α-helix	220-225	6
α-helix	226-230	5

Chain B: 12 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	14-26	13
β-strand	31-33	3	1
α-helix	34-48	15
α-helix	57-76	20
β-strand	81-86	6	1
α-helix	92-96	5
β-strand	97	1	2
β-strand	100	1	2
β-strand	131-136	6	1
α-helix	152-167	16
α-helix	182-194	13
β-strand	206-207	2	3
α-helix	216-218	3
α-helix	224-236	13
β-strand	240-242	3	4
β-strand	248-250	3	4
α-helix	252-257	6
α-helix	259-265	7
α-helix	268-269	2
β-strand	270	1	5
β-strand	271	1	6
β-strand	277	1	5
β-strand	281-282	2	3
β-strand	304	1	6
β-strand	305	1	3
α-helix	307-315	9
β-strand	334-335	2	3

Chain C: 19 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-24	16
α-helix	26-41	16
β-strand	46-47	2	7
α-helix	48-62	15
α-helix	69-79	11
α-helix	80-84	5
β-strand	86-91	6	7
α-helix	95-98	4
β-strand	122-127	6	7
α-helix	130-131	2
α-helix	135-145	11
α-helix	147-150	4
α-helix	152-154	3
α-helix	178-194	17
β-strand	199-200	2	8
α-helix	201-208	8
α-helix	209-211	3
α-helix	218-220	3
α-helix	227-236	10
β-strand	240-244	5	8
β-strand	247	1	9
β-strand	251	1	9
β-strand	254-258	5	8
α-helix	260-265	6
α-helix	268-279	12
α-helix	283-286	4
α-helix	290-297	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Non-structural maintenance of chromosome element 4	A	protein	402	Saccharomyces cerevisiae S288C	P43124 (AlphaFold model)
Non-structural maintenance of chromosomes element 1	B	protein	336	Saccharomyces cerevisiae S288C	Q07913 (AlphaFold model)
Non-structural maintenance of chromosome element 3	C	protein	303	Saccharomyces cerevisiae S288C	Q05541 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7YMD_1 Non-structural maintenance of chromosome element 4 (chains A)
MSSTVISRKRRNSTVTEPDSSGETRKQKKSRSDEKSSSSKDGDPQLEFKVLQGYRDLESE
MHKGRAQVTRTGDIGVAMDNLNAVDSLFNKVIGIKNNGLFAHDARAMVSISELAQISVRN
LKFDDSRSMVNLENIVNSLKRYMLKEHFKLNNIAENRNDLTLAADEQSAADQQEESDGDI
DRTPDDNHTDKATSSFKATSMRHSYLQQFSHYNEFSQFNWFRIGALYNTISKNAPITDHL
MGPLSIEKKPRVLTQRRRNNDQVGEKITAEKITQHSLNSTQQETTPEQVKKCFKKLSKKL
GPEGSINLFKFIIDPNSFSRSIENLFYTSFLIKEGKLLMEHDEEGLPTIKIKQSISHTDS
RSKEIERQRRRAAHQNHIIFQMDMPTWRKLIKKYNITSPFLD

Sequence of entity 2 (B), FASTA

>7YMD_2 Non-structural maintenance of chromosomes element 1 (chains B)
MEVHEEQVSAPVTGDATAKYLLQYILSARGICHENALILALMRLETDASTLNTEWSIQQW
VDKLNDYINAINVKLNLLGYKIIRINHGIGRNAVTLKAKQNFESFEDNTAIRAHNNDYAV
LQSIVLPESNRFFVYVNLASTEETKLATRFNQNEIEFMKWAIEQFMISGETIVEGPALET
SIIVKEVNRILVAATGDSNLAKWRKFSTFTVGSTNLFQFQELTATDIEDLLLRLCELKWF
YRTQEGKFGIDLRCIAELEEYLTSMYNLNTCQNCHKLAIQGVRCGNESCREENEETGENS
LSQIWHVDCFKHYITHVSKNCDRCGSSLITEGVYVI

Sequence of entity 3 (C), FASTA

>7YMD_3 Non-structural maintenance of chromosome element 3 (chains C)
MSSIDNDSDVDLTEDLAVAKIVKENPVARKMVRYILSRGESQNSIITRNKLQSVIHEAAR
EENIAKPSFSKMFMDINAILYNVYGFELQGLPSKNNMNAGGNGSNSNTNKSMPEPLGHRA
QKFILLNNVPHSKNFDDFKILQSAHTYEELIVTGEYIGDDIASGTSNTLESKLSTDRDLV
YKGVLSVILCIVFFSKNNILHQELIKFLETFGIPSDGSKIAILNITIEDLIKSLEKREYI
VRLEEKSDTDGEVISYRIGRRTQAELGLESLEKLVQEIMGLEKEQTKSLHDDIIKSIGDS
YSI

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). DOI 10.1038/s41594-024-01319-1 · PubMed

Other PDB entries of the same protein (UniProt P43124 (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
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
7QCD 8.0 Å, CryoEM structure of the Smc5/6-holocomplex (composite structure)

Browse structure collections

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