9S53: Kinetochore-associated protein DSN1

Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain. Determined by electron microscopy at 6.5 Å resolution. Released 8 Apr 2026.

Method: Electron microscopy
Resolution: 6.5 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 4
Atoms: 4,985
Mol. weight: 148.19 kDa
Released: 8 Apr 2026

Explore 9S53 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S53 contains 32 α-helices and 4 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 Ds: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	231-243	13
α-helix	247-254	8
α-helix	271-273	3
α-helix	275-277	3
α-helix	285-309	25
α-helix	340-355	16
α-helix	436-467	32
α-helix	471-481	11

Chain Mt: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	6-16	11
α-helix	20-48	29
β-strand	52	1	1
β-strand	55	1	1
α-helix	58-86	29
α-helix	87-92	6
α-helix	93-95	3
α-helix	96-99	4
α-helix	107-109	3
α-helix	117-150	34

Chain Nn: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	7-27	21
α-helix	30-36	7
α-helix	38-42	5
α-helix	44-75	32
α-helix	78-97	20
α-helix	101-103	3
α-helix	110-112	3
α-helix	116-152	37

Chain Ns: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	9-10	2	2
α-helix	13-34	22
α-helix	44-65	22
β-strand	68-69	2	2
α-helix	80-85	6
α-helix	88-91	4
α-helix	93-95	3
α-helix	99-158	60

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinetochore-associated protein DSN1	Ds	protein	576	Saccharomyces cerevisiae S288C	P40568 (AlphaFold model)
Kinetochore-associated protein MTW1	Mt	protein	289	Saccharomyces cerevisiae S288C	P39731 (AlphaFold model)
Kinetochore-associated protein NNF1	Nn	protein	201	Saccharomyces cerevisiae S288C	P47149 (AlphaFold model)
Kinetochore-associated protein NSL1	Ns	protein	216	Saccharomyces cerevisiae S288C	Q12143 (AlphaFold model)

Sequence of entity 1 (Ds), FASTA

>9S53_1 Kinetochore-associated protein DSN1 (chains Ds)
MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFE
NKQSVSNLSPDLKFKRHKNKHIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSG
DATANATANATANATANVNASAMPAPYMPYYYYYHPMNAPTPAMIPYPGSPMHSIMPNSS
LQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKS
IGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRS
LHKLELKAKNQEEEGELEHLTKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAI
DWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDDDDDEVDYSEIQRSRRKFSER
RKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSF
SSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIE
TMRKISSETDDDHSQVINPQQLLKGLSLSFSKKLDL

Sequence of entity 2 (Mt), FASTA

>9S53_2 Kinetochore-associated protein MTW1 (chains Mt)
MSAPTMRSTSILTEHLGYPPISLVDDIINAVNEIMYKCTAAMEKYLLSKSKIGEEDYGEE
IKSGVAKLESLLENSVDKNFDKLELYVLRNVLRIPEEYLDANVFRLENQKDLVIVDENEL
KKSEEKLREKVNDVELAFKKNEMLLKRVTKVKRLLFTIRGFKQKLNELLKCKDDVQLQKI
LESLKPIDDTMTLLTDSLRKLYVDSESTSSTEEVEALLQRLKTNGKQNNKDFRTRYIDIR
TNNVLRKLGLLGDKEDEKQSAKPDARTQAGDIVSIDIEEPQLDLLDDVL

Sequence of entity 3 (Nn), FASTA

>9S53_3 Kinetochore-associated protein NNF1 (chains Nn)
MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEF
WTELCQREFKEIMEERNVEQKLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVE
CHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVEVEKNEIGKMYDEYLGSHTDQ
PANVLLVQSLNDMVLELKENY

Sequence of entity 4 (Ns), FASTA

>9S53_4 Kinetochore-associated protein NSL1 (chains Ns)
MSQGQSKKLDVTVEQLRSIYHQFHDILEEKTDLHLPKKEYDDDAVRREVQIQLQEFLLSA
MTMASKSLEVVNADTVGKTVKQLIMESQEKYMEPFDLDLNEQVRKMYQEWEDETVKVAQL
RQTGPAKINEVYNNSKDEYLAQLDGRIGVLQARMMQQQSADHDDSTDDADDHINWEHIKQ
DYVASLNELYQTQQDLPKVRYNVEKVKRLMDFLEED

Primary citation

Assembly and phosphoregulatory mechanisms of the budding yeast outer kinetochore KMN complex. Turner, N.N., Zhang, Z., Yang, J. et al. J Cell Biol (2026) 225. DOI 10.1083/jcb.202506015 · PubMed

Other PDB entries of the same protein (UniProt P40568 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5T6J 1.75 Å, Structure of the MIND Complex Shows a Regulatory Focus of Yeast Kinetochore Assembly
6MJE 2.5 Å, Structure of Candida glabrata Csm1: S. cerevisiae Dsn1 complex
9S4Q 4.9 Å, Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the…
9S5N 7.2 Å, Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the…

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