8Q5H: Human KMN network

Human KMN network (outer kinetochore). Determined by electron microscopy at 4.5 Å resolution. Released 14 Feb 2024.

Method: Electron microscopy
Resolution: 4.5 Å
Organism: Homo sapiens
Chains: 7
Atoms: 9,574
Mol. weight: 185.97 kDa
Released: 14 Feb 2024

Explore 8Q5H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q5H contains 44 α-helices and 23 β-strands across 7 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 4: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	132-147	16
β-strand	149-151	3	1
β-strand	160-164	5	1
β-strand	171-175	5	1
α-helix	182-192	11

Chain 5: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	124-137	14
α-helix	138-142	5
β-strand	144-149	6	2
β-strand	153-158	6	2
β-strand	170-176	7	2
β-strand	182-188	7	2
α-helix	195-203	9
α-helix	208-220	13
α-helix	221-223	3

Chain A: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	9-13	5
α-helix	17-49	33
α-helix	57-85	29
α-helix	86-90	5
α-helix	100-105	6
α-helix	111-169	59
α-helix	174-204	31

Chain B: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	34-51	18
α-helix	54-64	11
α-helix	70-97	28
α-helix	101-115	15
α-helix	129-188	60
α-helix	190-200	11
α-helix	202-204	3

Chain D: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	130-149	20
α-helix	150-152	3
β-strand	156	1	3
β-strand	159	1	3
α-helix	162-182	21
α-helix	189-191	3
α-helix	204-244	41
α-helix	265-269	5
α-helix	274-326	53
α-helix	332-337	6

Chain K: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2135-2140	6	4
β-strand	2144-2149	6	4
β-strand	2154-2160	7	4
β-strand	2176	1	5
β-strand	2177-2184	8	4
α-helix	2193-2207	15
α-helix	2212-2215	4
β-strand	2218	1	5
α-helix	2222-2253	32
β-strand	2258-2259	2	6
β-strand	2265-2271	7	6
β-strand	2276-2282	7	6
β-strand	2295-2301	7	6
α-helix	2306-2315	10
α-helix	2322-2330	9
α-helix	2331-2336	6
α-helix	2339-2341	3

Chain N: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	38-39	2	7
α-helix	44-53	10
α-helix	55-61	7
α-helix	69-87	19
β-strand	88-89	2	7
β-strand	90	1	8
β-strand	93	1	8
α-helix	105-150	46
α-helix	163-165	3
α-helix	167-212	46
α-helix	215-221	7
α-helix	265-269	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Kinetochore protein Spc24	4	protein	89	Homo sapiens	Q8NBT2 (AlphaFold model)
Kinetochore protein Spc25	5	protein	139	Homo sapiens	Q9HBM1 (AlphaFold model)
Protein MIS12 homolog	A	protein	205	Homo sapiens	Q9H081 (AlphaFold model)
Polyamine-modulated factor 1	B	protein	205	Homo sapiens	Q6P1K2 (AlphaFold model)
Kinetochore-associated protein DSN1 homolog	D	protein	362	Homo sapiens	Q9H410
Kinetochore scaffold 1	K	protein	329	Homo sapiens	Q8NG31
Kinetochore-associated protein NSL1 homolog	N	protein	281	Homo sapiens	Q96IY1

Sequence of entity 1 (4), FASTA

>8Q5H_1 Kinetochore protein Spc24 (chains 4)
MELKEIEADLERQEKEVDEDTTVTIPSAVYVAQLYHQVSKIEWDYECEPGMVKGIHHGPS
VAQPIHLDSTQLSRKFISDYLWSLVDTEW

Sequence of entity 2 (5), FASTA

>8Q5H_2 Kinetochore protein Spc25 (chains 5)
MKQELEVLTANIQDLKEEYSRKKETISTANKANAERLKRLQKSADLYKDRLGLEIRKIYG
EKLQFIFTNIDPKNPESPFMFSLHLNEARDYEVSDSAPHLEGLAEFQENVRKTNNFSAFL
ANVRKAFTATVYNHHHHHH

Sequence of entity 3 (A), FASTA

>8Q5H_3 Protein MIS12 homolog (chains A)
MSVDPMTYEAQFFGFTPQTCMLRIYIAFQDYLFEVMQAVEQVILKKLDGIPDCDISPVQI
RKCTEKFLCFMKGHFDNLFSKMEQLFLQLILRIPSNILLPEDKCKETPYSEEDFQHLQKE
IEQLQEKYKTELCTKQALLAELEEQKIVQAKLKQTLTFFDELHNVGRDHGTSDFRESLVS
LVQNSRKLQNIRDNVEKESKRLKIS

Sequence of entity 4 (B), FASTA

>8Q5H_4 Polyamine-modulated factor 1 (chains B)
MAEASSANLGSGCEEKRHEGSSSESVPPGTTISRVKLLDTMVDTFLQKLVAAGSYQRFTD
CYKCFYQLQPAMTQQIYDKFIAQLQTSIREEISDIKEEGNLEAVLNALDKIVEEGKVRKE
PAWRPSGIPEKDLHSVMAPYFLQQRDTLRRHVQKQEAENQQLADAVLAGRRQVEELQLQV
QAQQQAWQALHREQRELVAVLREPE

Sequence of entity 5 (D), FASTA

>8Q5H_5 Kinetochore-associated protein DSN1 homolog (chains D)
MTSVTRSEIIDEKGPVMSKTHDHQLESSLSPVEVFAKTSASLEMNQGVSEERIHLGSSPK
KGGNCDLSHQERLQSKSLHLSPQEQSASYQDRRQSWRRASMKETNRRKSLHPIHQGITEL
SRSISVDLAESKRLGCLLLSSFQFSIQKLEPFLRDTKGFSLESFRAKASSLSEELKHFAD
GLETDGTLQKCFEDSNGKASDFSLEASVAEMKEYITKFSLERQTWDQLLLHYQQEAKEIL
SRGSTEAKITEVKVEPMTYLGSSQNEVLNTKPDYQKILQNQSKVFDCMELVMDELQGSVK
QLQAFMDESTQCFQKVSVQLGKRSMQQLDPSPARKLLKLQLQNPPAIHGSGSGSCQHHHH
HH

Sequence of entity 6 (K), FASTA

>8Q5H_6 Kinetochore scaffold 1 (chains K)
GAMGGSMGKLVQSAQNEREKLQIKIDEMDKILKKIDNCLTEMETETKNLEDEEKNNPVEE
WDSEMRAAEKELEQLKTEEEELQRNLLELEVQKEQTLAQIDFMQKQRNRTEELLDQLSLS
EWDVVEWSDDQAVFTFVYDTIQLTITFEESVVGFPFLDKRYRKIVDVNFQSLLDEDQAPP
SSLLVHKLIFQYVEEKESWKKTCTTQHQLPKMLEEFSLVVHHCRLLGEEIEYLKRWGPNY
NLMNIDINNNELRLLFSSSAAFAKFEITLFLSAYYPSVPLPSTIQNHVGNTSQDDIATIL
SKVPLENNYLKNVVKQIYQDLFQDCHFYH

Sequence of entity 7 (N), FASTA

>8Q5H_7 Kinetochore-associated protein NSL1 homolog (chains N)
MAGSPELVVLDPPWDKELAAGTESQALVSATPREDFRVRCTSKRAVTEMLQLCGRFVQKL
GDALPEEIREPALRDAQWTFESAVQENISINGQAWQEASDNCFMDSDIKVLEDQFDEIIV
DIATKRKQYPRKILECVIKTIKAKQEILKQYHPVVHPLDLKYDPDPAPHMENLKCRGETV
AKEISEAMKSLPALIEQGEGFSQVLRMQPVIHLQRIHQEVFSSCHRKPDAKPENFITQIE
TTPTETASRKTSDMVLKRKQTKDCPQRKWYPLRPKKINLDT

Primary citation

Structure of the human KMN complex and implications for regulation of its assembly. Polley, S., Raisch, T., Ghetti, S. et al. Nat Struct Mol Biol (2024) 31:861-873. DOI 10.1038/s41594-024-01230-9 · PubMed

Other PDB entries of the same protein (UniProt Q8NBT2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VE7 2.88 Å, Crystal structure of a bonsai version of the human Ndc80 complex
8PPR 3.0 Å, Structure of the human outer kinetochore KMN network complex
3IZ0 8.6 Å, Human Ndc80 Bonsai Decorated Microtubule

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