9S4Q: Kinetochore-associated protein NNF1

Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex lacking the Mis12c(Mtw1c) head 2 domain. Determined by electron microscopy at 4.9 Å resolution. Released 8 Apr 2026.

Method: Electron microscopy
Resolution: 4.9 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 8
Atoms: 9,689
Mol. weight: 302.15 kDa
Released: 8 Apr 2026

Explore 9S4Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S4Q contains 55 α-helices and 26 β-strands across 8 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 24: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	153-168	16
β-strand	170-173	4	5
β-strand	178-182	5	5
β-strand	189-193	5	5
α-helix	200-212	13

Chain 25: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	125-131	7
α-helix	134-145	12
β-strand	148-151	4	6
β-strand	159-162	4	6
β-strand	163	1	7
β-strand	169	1	7
β-strand	170-173	4	8
β-strand	181-185	5	8
α-helix	190-198	9
α-helix	199-203	5
α-helix	206-220	15

Chain Ds: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	435-467	33
α-helix	471-481	11
α-helix	487-489	3
α-helix	493-545	53
α-helix	559-575	17

Chain Kl: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	720-731	12
β-strand	733-739	7	2
β-strand	742-747	6	2
α-helix	748-750	3
β-strand	753-757	5	2
α-helix	759-762	4
α-helix	766-768	3
β-strand	770-772	3	2
α-helix	783-793	11
α-helix	798-800	3
α-helix	801-809	9
α-helix	814-816	3
α-helix	817-823	7
β-strand	828-832	5	4
β-strand	838-846	9	4
β-strand	851-858	8	4
α-helix	859-867	9
β-strand	873-881	9	4
α-helix	892-901	10
β-strand	912-915	4	4

Chain Mt: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	6-16	11
α-helix	20-48	29
β-strand	51-52	2	1
β-strand	55-56	2	1
α-helix	58-86	29
α-helix	87-91	5
α-helix	93-95	3
α-helix	97-100	4
α-helix	107-109	3
α-helix	117-168	52
α-helix	175-184	10
α-helix	187-208	22
α-helix	211-218	8
α-helix	232-247	16
β-strand	277-278	2	2
α-helix	282-288	7

Chain Nn: 10 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	116-174	59
α-helix	177-179	3
α-helix	186-198	13

Chain Ns: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	99-159	61
α-helix	167-171	5
α-helix	175-213	39

Chain Zw: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	282-288	7
α-helix	289-293	5
α-helix	298-300	3
β-strand	301-307	7	3
β-strand	312-317	6	3
β-strand	322-327	6	3
β-strand	338-345	8	3
β-strand	348-351	4	3
α-helix	353-363	11
α-helix	371-384	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinetochore-associated protein NNF1	Nn	protein	201	Saccharomyces cerevisiae S288C	P47149 (AlphaFold model)
Kinetochore-associated protein MTW1	Mt	protein	289	Saccharomyces cerevisiae S288C	P39731 (AlphaFold model)
Outer kinetochore KNL1 complex subunit KRE28	Zw	protein	420	Saccharomyces cerevisiae S288C	Q04431 (AlphaFold model)
Outer kinetochore KNL1 complex subunit SPC105	Kl	protein	474	Saccharomyces cerevisiae S288C	P53148 (AlphaFold model)
Kinetochore-associated protein DSN1	Ds	protein	576	Saccharomyces cerevisiae S288C	P40568
Kinetochore protein SPC24	24	protein	213	Saccharomyces cerevisiae S288C	Q04477
Kinetochore protein SPC25	25	protein	221	Saccharomyces cerevisiae S288C	P40014
Kinetochore-associated protein NSL1	Ns	protein	216	Saccharomyces cerevisiae S288C	Q12143

Sequence of entity 1 (Nn), FASTA

>9S4Q_1 Kinetochore-associated protein NNF1 (chains Nn)
MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEF
WTELCQREFKEIMEERNVEQKLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVE
CHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVEVEKNEIGKMYDEYLGSHTDQ
PANVLLVQSLNDMVLELKENY

Sequence of entity 2 (Mt), FASTA

>9S4Q_2 Kinetochore-associated protein MTW1 (chains Mt)
MSAPTMRSTSILTEHLGYPPISLVDDIINAVNEIMYKCTAAMEKYLLSKSKIGEEDYGEE
IKSGVAKLESLLENSVDKNFDKLELYVLRNVLRIPEEYLDANVFRLENQKDLVIVDENEL
KKSEEKLREKVNDVELAFKKNEMLLKRVTKVKRLLFTIRGFKQKLNELLKCKDDVQLQKI
LESLKPIDDTMTLLTDSLRKLYVDSESTSSTEEVEALLQRLKTNGKQNNKDFRTRYIDIR
TNNVLRKLGLLGDKEDEKQSAKPDARTQAGDIVSIDIEEPQLDLLDDVL

Sequence of entity 3 (Zw), FASTA

>9S4Q_3 Outer kinetochore KNL1 complex subunit KRE28 (chains Zw)
MDTGSASIKDYETVLTDIEDSIAVSSEEVLNNQELRLKNTLHEITSSILAINEENKFVNP
LRNDESLDVEGKEVFVNPKILSAKIKEFNKLMELLKLTYLEQETLDYFFRFTLSSTKPLQ
LDSEKDPQFVKLNERVNDLKEEISNVQESKIEQIKAEIQETGHNFAERQDLINELYLEAT
GDIENCWDSLNELKNLTNKEDKNMMGEKDTILNSSDSDDFVEETYTNWQKLLFLQKQNQR
LTKELKEMHEVKNQIIRKGEQSKKEDSGHLMANESELCQSINLLTKFWEKHFLLKGSKTT
ILNFEIFTQLGKVQFEIKDMQYIIAISLSDLKRPMIKDITILQKAGGNIVTDIEASSKFN
NKYRNNTKVQIFEVMDDIISELTNEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK

Sequence of entity 4 (Kl), FASTA

>9S4Q_4 Outer kinetochore KNL1 complex subunit SPC105 (chains Kl)
MSGIALPTQDYTLREFINEVGVGFLDTKLIDDLDKKVNFPLNSFNFVENQRIDNVFSAFY
IDIPILEVEAFRCKELWRSINESKDKFKDFEAQIDKSHPPLLLQEYFSSDEKMKQLMRDQ
LQLVKGYSKLEAAMEWYEWRKKQLNGLELILAENLNTLKREYEKLNEEVEKVNSIRGKIR
KLNEAIKEEIRSLKNLPSDSYKPTLMNRIKIEAFKQELMEHSISLSSSNDFTQEMRSLKL
AIAKKSNDILTLRSEVASIDKKIEKRKLFTRFDLPKLRDTLKILESLTGVRFLKFSKATL
SIAFLQLDDLRVDINLANFKNNPLSSMKVMNDSNNDDMSYHLFTMLLKNVEAEHQDSMLS
NLFFAMKKWRPLLKYIKLLKLLFPVKITQTEEEEALLQFKDYDRRNKTAFFYVISLVSFA
QGVFSENGQIPMKVHISTQQDYSPSREVLSDRITHKISGVLPSFTKSRIHLEFT

Sequence of entity 5 (Ds), FASTA

>9S4Q_5 Kinetochore-associated protein DSN1 (chains Ds)
MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFE
NKQSVSNLSPDLKFKRHKNKHIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSG
DATANATANATANATANVNASAMPAPYMPYYYYYHPMNAPTPAMIPYPGSPMHSIMPNSS
LQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKS
IGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRS
LHKLELKAKNQEEEGELEHLTKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAI
DWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDDDDDEVDYSEIQRSRRKFSER
RKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSF
SSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIE
TMRKISSETDDDHSQVINPQQLLKGLSLSFSKKLDL

Sequence of entity 6 (24), FASTA

>9S4Q_6 Kinetochore protein SPC24 (chains 24)
MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARISKEHSKVSESN
KKLNAERINVAKLEGDLEYTNEESNEFGSKDELVKLLKDLDGLERNIVSLRSELDEKMKL
YLKDSEIISTPNGSKIKAKVIEPELEEQSAVTPEANENILKLKLYRSLGVILDLENDQVL
INRKNDGNIDILPLDNNLSDFYKTKYIWERLGK

Sequence of entity 7 (25), FASTA

>9S4Q_7 Kinetochore protein SPC25 (chains 25)
MASIDAFSDLERRMDGFQKDVAQVLARQQNHARQQLQQFQAEMRQLHNQHQHLIDELQRL
ATQRTALQQQIHAAQQATNTTREQWRSYHERESELSRRQSTLAAQSRELDSLLQQRGKEC
VQLRARWAAQSGNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHV
IGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL

Sequence of entity 8 (Ns), FASTA

>9S4Q_8 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 P47149 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9S53 6.5 Å, Cryo-EM structure of the base of the Saccharomyces cerevisiae KMN junction complex…
9S5N 7.2 Å, Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the…

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