9S5N: Kinetochore-associated protein NNF1

Cryo-EM structure of the Saccharomyces cerevisiae KMN junction complex containing the Mis12c(Mtw1c) head 2 domain. Determined by electron microscopy at 7.2 Å resolution. Released 8 Apr 2026.

Method
Electron microscopy
Resolution
7.2 Å
Organisms
Saccharomyces cerevisiae, Saccharomyces cerevisiae S288C
Chains
8
Atoms
11,249
Mol. weight
302.15 kDa
Released
8 Apr 2026

Explore 9S5N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S5N contains 61 α-helices and 28 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

ElementResiduesLengthSheet
α-helix153-16715
β-strand170-17345
β-strand178-18365
β-strand188-19365
α-helix200-21213
Chain 25: 5 helices, 6 β-strands
ElementResiduesLengthSheet
α-helix125-1317
α-helix134-14512
β-strand148-15146
β-strand159-16246
β-strand16317
β-strand16917
β-strand170-17348
β-strand181-18558
α-helix190-1989
α-helix199-2035
α-helix206-22015
Chain Ds: 10 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix231-24414
α-helix247-2548
α-helix271-2788
α-helix285-30925
α-helix340-35415
α-helix436-46732
α-helix470-48112
α-helix487-4893
α-helix493-54553
α-helix559-57517
Chain Kl: 9 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix720-73112
β-strand733-74082
β-strand743-74752
α-helix748-7503
β-strand753-75752
α-helix759-7624
β-strand770-77232
α-helix781-79313
α-helix798-8003
α-helix801-81212
α-helix815-82511
β-strand828-83254
β-strand838-84694
β-strand851-85884
α-helix859-8679
β-strand873-88194
α-helix889-90113
β-strand912-91654
Chain Mt: 12 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix2-43
α-helix6-1611
α-helix20-4829
β-strand51-5221
β-strand55-5621
α-helix58-8629
α-helix87-926
α-helix96-1016
α-helix117-17054
α-helix175-18410
α-helix187-20923
α-helix211-2199
α-helix232-24716
β-strand277-28042
α-helix282-2887
Chain Nn: 10 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix7-2721
α-helix30-367
α-helix38-425
α-helix44-7532
α-helix78-9720
α-helix101-1033
α-helix110-1123
α-helix116-17459
α-helix177-1793
α-helix186-20015
Chain Ns: 8 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand919
α-helix13-3422
α-helix44-6522
β-strand6819
α-helix80-856
α-helix88-914
α-helix93-964
α-helix99-15961
α-helix167-1715
α-helix175-21339
Chain Zw: 5 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix281-2888
α-helix289-2935
α-helix295-2973
β-strand302-30763
β-strand312-31653
β-strand322-32763
β-strand338-34583
β-strand348-35143
α-helix353-36311
α-helix371-38313

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Kinetochore-associated protein NNF1Nnprotein201Saccharomyces cerevisiaeP47149 (AlphaFold model)
Kinetochore-associated protein MTW1Mtprotein289Saccharomyces cerevisiae S288CP39731 (AlphaFold model)
Outer kinetochore KNL1 complex subunit KRE28Zwprotein420Saccharomyces cerevisiae S288CQ04431 (AlphaFold model)
Outer kinetochore KNL1 complex subunit SPC105Klprotein474Saccharomyces cerevisiae S288CP53148 (AlphaFold model)
Kinetochore-associated protein DSN1Dsprotein576Saccharomyces cerevisiae S288CP40568
Kinetochore protein SPC2424protein213Saccharomyces cerevisiae S288CQ04477
Kinetochore protein SPC2525protein221Saccharomyces cerevisiae S288CP40014
Kinetochore-associated protein NSL1Nsprotein216Saccharomyces cerevisiae S288CQ12143
Sequence of entity 1 (Nn), FASTA
>9S5N_1 Kinetochore-associated protein NNF1 (chains Nn)
MVNSHGIRYIRLKQVFNRALDQSISKLQSWDKVSSCFPQYVNSKQGAINVANCQRQLTEF
WTELCQREFKEIMEERNVEQKLNELDELILEAKERYTDRDQDEVNKGPAIDELSSKELVE
CHLYSQRMHAIHEIDERLAKVNEMNDQLAQELKDLETQVEVEKNEIGKMYDEYLGSHTDQ
PANVLLVQSLNDMVLELKENY
Sequence of entity 2 (Mt), FASTA
>9S5N_2 Kinetochore-associated protein MTW1 (chains Mt)
MSAPTMRSTSILTEHLGYPPISLVDDIINAVNEIMYKCTAAMEKYLLSKSKIGEEDYGEE
IKSGVAKLESLLENSVDKNFDKLELYVLRNVLRIPEEYLDANVFRLENQKDLVIVDENEL
KKSEEKLREKVNDVELAFKKNEMLLKRVTKVKRLLFTIRGFKQKLNELLKCKDDVQLQKI
LESLKPIDDTMTLLTDSLRKLYVDSESTSSTEEVEALLQRLKTNGKQNNKDFRTRYIDIR
TNNVLRKLGLLGDKEDEKQSAKPDARTQAGDIVSIDIEEPQLDLLDDVL
Sequence of entity 3 (Zw), FASTA
>9S5N_3 Outer kinetochore KNL1 complex subunit KRE28 (chains Zw)
MDTGSASIKDYETVLTDIEDSIAVSSEEVLNNQELRLKNTLHEITSSILAINEENKFVNP
LRNDESLDVEGKEVFVNPKILSAKIKEFNKLMELLKLTYLEQETLDYFFRFTLSSTKPLQ
LDSEKDPQFVKLNERVNDLKEEISNVQESKIEQIKAEIQETGHNFAERQDLINELYLEAT
GDIENCWDSLNELKNLTNKEDKNMMGEKDTILNSSDSDDFVEETYTNWQKLLFLQKQNQR
LTKELKEMHEVKNQIIRKGEQSKKEDSGHLMANESELCQSINLLTKFWEKHFLLKGSKTT
ILNFEIFTQLGKVQFEIKDMQYIIAISLSDLKRPMIKDITILQKAGGNIVTDIEASSKFN
NKYRNNTKVQIFEVMDDIISELTNEENLYFQSWSHPQFEKGGGSGGGSGGGSWSHPQFEK
Sequence of entity 4 (Kl), FASTA
>9S5N_4 Outer kinetochore KNL1 complex subunit SPC105 (chains Kl)
MSGIALPTQDYTLREFINEVGVGFLDTKLIDDLDKKVNFPLNSFNFVENQRIDNVFSAFY
IDIPILEVEAFRCKELWRSINESKDKFKDFEAQIDKSHPPLLLQEYFSSDEKMKQLMRDQ
LQLVKGYSKLEAAMEWYEWRKKQLNGLELILAENLNTLKREYEKLNEEVEKVNSIRGKIR
KLNEAIKEEIRSLKNLPSDSYKPTLMNRIKIEAFKQELMEHSISLSSSNDFTQEMRSLKL
AIAKKSNDILTLRSEVASIDKKIEKRKLFTRFDLPKLRDTLKILESLTGVRFLKFSKATL
SIAFLQLDDLRVDINLANFKNNPLSSMKVMNDSNNDDMSYHLFTMLLKNVEAEHQDSMLS
NLFFAMKKWRPLLKYIKLLKLLFPVKITQTEEEEALLQFKDYDRRNKTAFFYVISLVSFA
QGVFSENGQIPMKVHISTQQDYSPSREVLSDRITHKISGVLPSFTKSRIHLEFT
Sequence of entity 5 (Ds), FASTA
>9S5N_5 Kinetochore-associated protein DSN1 (chains Ds)
MSLEPTQTVSGTPPMLHQRTHKQVYPLRMETIPILESDSKATLQSNEPTQKDEEETEYFE
NKQSVSNLSPDLKFKRHKNKHIQGFPTLGERLDNLQDIKKAKRVENFNSSAPIADDNHSG
DATANATANATANATANVNASAMPAPYMPYYYYYHPMNAPTPAMIPYPGSPMHSIMPNSS
LQPFYSQPTAAGGPDMTTPQNISSSQQLLPAPQLFPYGSFHQQQLQQPHYIQRTRERKKS
IGSQRGRRLSMLASQANGGSTIISPHKDIPEEDFYTVVGNASFGKNLQIRQLFNWCLMRS
LHKLELKAKNQEEEGELEHLTKKSKLESTKAETDYVDPKRLAMVIIKEFVDDLKKDHIAI
DWEDEEKYEDEDEEKILDNTENYDDTELRQLFQENDDDDDDDDEVDYSEIQRSRRKFSER
RKALPKEPKKLLPNSKNVENTKNLSILTSKVNAIKNEVKEWAVTLDTSRPDLEWQELTSF
SSQPLEPLSDTEEPDLAIADVETKLETKVDELRYQSHILNSHSLALNEITNSKVNKLNIE
TMRKISSETDDDHSQVINPQQLLKGLSLSFSKKLDL
Sequence of entity 6 (24), FASTA
>9S5N_6 Kinetochore protein SPC24 (chains 24)
MSQKDNLLDNPVEFLKEVRESFDIQQDVDAMKRIRHDLDVIKEESEARISKEHSKVSESN
KKLNAERINVAKLEGDLEYTNEESNEFGSKDELVKLLKDLDGLERNIVSLRSELDEKMKL
YLKDSEIISTPNGSKIKAKVIEPELEEQSAVTPEANENILKLKLYRSLGVILDLENDQVL
INRKNDGNIDILPLDNNLSDFYKTKYIWERLGK
Sequence of entity 7 (25), FASTA
>9S5N_7 Kinetochore protein SPC25 (chains 25)
MASIDAFSDLERRMDGFQKDVAQVLARQQNHARQQLQQFQAEMRQLHNQHQHLIDELQRL
ATQRTALQQQIHAAQQATNTTREQWRSYHERESELSRRQSTLAAQSRELDSLLQQRGKEC
VQLRARWAAQSGNDAAEVALYERLLQLRVLPGASDVHDVRFVFGDDSRCWIEVAMHGDHV
IGNSHPALDPKSRATLEHVLTVQGDLAAFLVVARDMLLASL
Sequence of entity 8 (Ns), FASTA
>9S5N_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:

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